diff --git a/packages/@vue/cli-plugin-babel/migrator/index.js b/packages/@vue/cli-plugin-babel/migrator/index.js
index 9263c767ed..daae8778fc 100644
--- a/packages/@vue/cli-plugin-babel/migrator/index.js
+++ b/packages/@vue/cli-plugin-babel/migrator/index.js
@@ -1,14 +1,20 @@
 const { chalk } = require('@vue/cli-shared-utils')
 
-module.exports = (api) => {
-  api.transformScript('babel.config.js', require('../codemods/usePluginPreset'))
+module.exports = api => {
+  api.transformScript(
+    'babel.config.js',
+    require('../codemods/usePluginPreset')
+  )
 
   if (api.fromVersion('^3')) {
-    api.extendPackage({
-      dependencies: {
-        'core-js': '^3.6.4'
-      }
-    }, true)
+    api.extendPackage(
+      {
+        dependencies: {
+          'core-js': '^3.6.4'
+        }
+      },
+      { warnIncompatibleVersions: false }
+    )
 
     // TODO: implement a codemod to migrate polyfills
     api.exitLog(`core-js has been upgraded from v2 to v3.
diff --git a/packages/@vue/cli-plugin-eslint/migrator/index.js b/packages/@vue/cli-plugin-eslint/migrator/index.js
index aa00200496..08b03584e9 100644
--- a/packages/@vue/cli-plugin-eslint/migrator/index.js
+++ b/packages/@vue/cli-plugin-eslint/migrator/index.js
@@ -54,7 +54,7 @@ module.exports = async (api) => {
       Object.assign(newDeps, getDeps(api, 'prettier'))
     }
 
-    api.extendPackage({ devDependencies: newDeps }, true)
+    api.extendPackage({ devDependencies: newDeps }, { warnIncompatibleVersions: false })
 
     // in case anyone's upgrading from the legacy `typescript-eslint-parser`
     if (api.hasPlugin('typescript')) {
diff --git a/packages/@vue/cli-plugin-typescript/migrator/index.js b/packages/@vue/cli-plugin-typescript/migrator/index.js
index 6320111115..a28ea4d578 100644
--- a/packages/@vue/cli-plugin-typescript/migrator/index.js
+++ b/packages/@vue/cli-plugin-typescript/migrator/index.js
@@ -1,7 +1,10 @@
-module.exports = (api) => {
-  api.extendPackage({
-    devDependencies: {
-      typescript: require('../package.json').devDependencies.typescript
-    }
-  }, true)
+module.exports = api => {
+  api.extendPackage(
+    {
+      devDependencies: {
+        typescript: require('../package.json').devDependencies.typescript
+      }
+    },
+    { warnIncompatibleVersions: false }
+  )
 }
diff --git a/packages/@vue/cli/__tests__/Generator.spec.js b/packages/@vue/cli/__tests__/Generator.spec.js
index 7bbd4607aa..77a780cb95 100644
--- a/packages/@vue/cli/__tests__/Generator.spec.js
+++ b/packages/@vue/cli/__tests__/Generator.spec.js
@@ -73,6 +73,10 @@ fs.ensureDirSync(path.resolve(templateDir, '_vscode'))
 fs.writeFileSync(path.resolve(templateDir, '_vscode/config.json'), `{}`)
 fs.writeFileSync(path.resolve(templateDir, '_gitignore'), 'foo')
 
+beforeEach(() => {
+  logs.warn = []
+})
+
 test('api: extendPackage', async () => {
   const generator = new Generator('/', {
     pkg: {
@@ -376,6 +380,130 @@ test('api: extendPackage merge warn nonstrictly semver deps', async () => {
   })).toBe(true)
 })
 
+test('api: extendPackage + { merge: false }', async () => {
+  const generator = new Generator('/', {
+    pkg: {
+      name: 'hello',
+      list: [1],
+      vue: {
+        foo: 1,
+        bar: 2
+      }
+    },
+    plugins: [{
+      id: 'test',
+      apply: api => {
+        api.extendPackage(
+          {
+            name: 'hello2',
+            list: [2],
+            vue: {
+              foo: 2,
+              baz: 3
+            }
+          },
+          { merge: false }
+        )
+      }
+    }]
+  })
+
+  await generator.generate()
+
+  const pkg = JSON.parse(fs.readFileSync('/package.json', 'utf-8'))
+  expect(pkg).toEqual({
+    name: 'hello2',
+    list: [2],
+    vue: {
+      foo: 2,
+      baz: 3
+    }
+  })
+})
+
+test('api: extendPackage + { prune: true }', async () => {
+  const generator = new Generator('/', {
+    pkg: {
+      name: 'hello',
+      version: '0.0.0',
+      dependencies: {
+        foo: '1.0.0'
+      },
+      vue: {
+        bar: 1,
+        baz: 2
+      }
+    },
+    plugins: [{
+      id: 'test',
+      apply: api => {
+        api.extendPackage(
+          {
+            name: null,
+            dependencies: {
+              foo: null,
+              qux: '2.0.0'
+            },
+            vue: {
+              bar: null,
+              baz: 3
+            }
+          },
+          { prune: true }
+        )
+      }
+    }]
+  })
+
+  await generator.generate()
+
+  const pkg = JSON.parse(fs.readFileSync('/package.json', 'utf-8'))
+  expect(pkg).toEqual({
+    version: '0.0.0',
+    dependencies: {
+      qux: '2.0.0'
+    },
+    vue: {
+      baz: 3
+    }
+  })
+})
+
+test('api: extendPackage + { warnIncompatibleVersions: false }', async () => {
+  const generator = new Generator('/', {
+    pkg: {
+      devDependencies: {
+        eslint: '^4.0.0'
+      }
+    },
+    plugins: [{
+      id: 'test',
+      apply: api => {
+        api.extendPackage(
+          {
+            devDependencies: {
+              eslint: '^6.0.0'
+            }
+          },
+          { warnIncompatibleVersions: false }
+        )
+      }
+    }]
+  })
+
+  await generator.generate()
+  const pkg = JSON.parse(fs.readFileSync('/package.json', 'utf-8'))
+
+  // should not warn about the version conflicts
+  expect(logs.warn.length).toBe(0)
+  // should use the newer version
+  expect(pkg).toEqual({
+    devDependencies: {
+      eslint: '^6.0.0'
+    }
+  })
+})
+
 test('api: render fs directory', async () => {
   const generator = new Generator('/', { plugins: [
     {
diff --git a/packages/@vue/cli/lib/GeneratorAPI.js b/packages/@vue/cli/lib/GeneratorAPI.js
index 640f220858..8b0906e7dd 100644
--- a/packages/@vue/cli/lib/GeneratorAPI.js
+++ b/packages/@vue/cli/lib/GeneratorAPI.js
@@ -1,7 +1,7 @@
 const fs = require('fs')
 const ejs = require('ejs')
 const path = require('path')
-const merge = require('deepmerge')
+const deepmerge = require('deepmerge')
 const resolve = require('resolve')
 const { isBinaryFileSync } = require('isbinaryfile')
 const mergeDeps = require('./util/mergeDeps')
@@ -14,6 +14,23 @@ const isString = val => typeof val === 'string'
 const isFunction = val => typeof val === 'function'
 const isObject = val => val && typeof val === 'object'
 const mergeArrayWithDedupe = (a, b) => Array.from(new Set([...a, ...b]))
+function pruneObject (obj) {
+  if (typeof obj === 'object') {
+    for (const k in obj) {
+      if (!obj.hasOwnProperty(k)) {
+        continue
+      }
+
+      if (obj[k] == null) {
+        delete obj[k]
+      } else {
+        obj[k] = pruneObject(obj[k])
+      }
+    }
+  }
+
+  return obj
+}
 
 class GeneratorAPI {
   /**
@@ -176,15 +193,34 @@ class GeneratorAPI {
 
   /**
    * Extend the package.json of the project.
-   * Nested fields are deep-merged unless `{ merge: false }` is passed.
    * Also resolves dependency conflicts between plugins.
    * Tool configuration fields may be extracted into standalone files before
    * files are written to disk.
    *
    * @param {object | () => object} fields - Fields to merge.
-   * @param {boolean} forceNewVersion - Ignore version conflicts when updating dependency version
+   * @param {object} [options] - Options for extending / merging fields.
+   * @param {boolean} [options.prune=false] - Remove null or undefined fields
+   *    from the object after merging.
+   * @param {boolean} [options.merge=true] deep-merge nested fields, note
+   *    that dependency fields are always deep merged regardless of this option.
+   * @param {boolean} [options.warnIncompatibleVersions=true] Output warning
+   *    if two dependency version ranges don't intersect.
    */
-  extendPackage (fields, forceNewVersion) {
+  extendPackage (fields, options = {}) {
+    const extendOptions = {
+      prune: false,
+      merge: true,
+      warnIncompatibleVersions: true
+    }
+
+    // this condition statement is added for compatiblity reason, because
+    // in version 4.0.0 to 4.1.2, there's no `options` object, but a `forceNewVersion` flag
+    if (typeof options === 'boolean') {
+      extendOptions.warnIncompatibleVersions = !options
+    } else {
+      Object.assign(extendOptions, options)
+    }
+
     const pkg = this.generator.pkg
     const toMerge = isFunction(fields) ? fields(pkg) : fields
     for (const key in toMerge) {
@@ -197,18 +233,22 @@ class GeneratorAPI {
           existing || {},
           value,
           this.generator.depSources,
-          forceNewVersion
+          extendOptions
         )
-      } else if (!(key in pkg)) {
+      } else if (!extendOptions.merge || !(key in pkg)) {
         pkg[key] = value
       } else if (Array.isArray(value) && Array.isArray(existing)) {
         pkg[key] = mergeArrayWithDedupe(existing, value)
       } else if (isObject(value) && isObject(existing)) {
-        pkg[key] = merge(existing, value, { arrayMerge: mergeArrayWithDedupe })
+        pkg[key] = deepmerge(existing, value, { arrayMerge: mergeArrayWithDedupe })
       } else {
         pkg[key] = value
       }
     }
+
+    if (extendOptions.prune) {
+      pruneObject(pkg)
+    }
   }
 
   /**
diff --git a/packages/@vue/cli/lib/util/mergeDeps.js b/packages/@vue/cli/lib/util/mergeDeps.js
index b7b0bf5798..410f02f487 100644
--- a/packages/@vue/cli/lib/util/mergeDeps.js
+++ b/packages/@vue/cli/lib/util/mergeDeps.js
@@ -3,61 +3,93 @@ const { semver, warn } = require('@vue/cli-shared-utils')
 const tryGetNewerRange = require('./tryGetNewerRange')
 
 const extractSemver = r => r.replace(/^.+#semver:/, '')
-const injectSemver = (r, v) => semver.validRange(r) ? v : r.replace(/#semver:.+$/, `#semver:${v}`)
-
-module.exports = function resolveDeps (generatorId, to, from, sources, forceNewVersion) {
-  const res = Object.assign({}, to)
-  for (const name in from) {
-    const r1 = to[name]
-    const r2 = from[name]
-    const r2IsString = typeof r2 === 'string'
-    const sourceGeneratorId = sources[name]
-    const isValidURI = r2IsString && r2.match(/^(?:file|git|git\+ssh|git\+http|git\+https|git\+file|https?):/) != null
-    const isValidGitHub = r2IsString && r2.match(/^[^/]+\/[^/]+/) != null
+const injectSemver = (r, v) =>
+  semver.validRange(r) ? v : r.replace(/#semver:.+$/, `#semver:${v}`)
+
+const isValidRange = range => {
+  if (typeof range !== 'string') {
+    return false
+  }
+
+  const isValidSemver = !!semver.validRange(range)
+  const isValidGitHub = range.match(/^[^/]+\/[^/]+/) != null
+  const isValidURI =
+    range.match(
+      /^(?:file|git|git\+ssh|git\+http|git\+https|git\+file|https?):/
+    ) != null
+
+  return isValidSemver || isValidGitHub || isValidURI
+}
+
+module.exports = function mergeDeps (
+  generatorId,
+  sourceDeps,
+  depsToInject,
+  sources,
+  {
+    prune,
+    warnIncompatibleVersions
+  }
+) {
+  const result = Object.assign({}, sourceDeps)
+
+  for (const depName in depsToInject) {
+    const sourceRange = sourceDeps[depName]
+    const injectingRange = depsToInject[depName]
 
     // if they are the same, do nothing. Helps when non semver type deps are used
-    if (r1 === r2) continue
+    if (sourceRange === injectingRange) continue
+
+    if (prune && injectingRange == null) {
+      delete result[depName]
+    }
 
-    if (!isValidGitHub && !isValidURI && !semver.validRange(r2)) {
+    if (!isValidRange(injectingRange)) {
       warn(
-        `invalid version range for dependency "${name}":\n\n` +
-        `- ${r2} injected by generator "${generatorId}"`
+        `invalid version range for dependency "${depName}":\n\n` +
+          `- ${injectingRange} injected by generator "${generatorId}"`
       )
       continue
     }
 
-    if (!r1) {
-      res[name] = r2
-      sources[name] = generatorId
+    const sourceGeneratorId = sources[depName]
+    if (!sourceRange) {
+      result[depName] = injectingRange
+      sources[depName] = generatorId
     } else {
-      const r1semver = extractSemver(r1)
-      const r2semver = extractSemver(r2)
-      const r = tryGetNewerRange(r1semver, r2semver)
+      const sourceRangeSemver = extractSemver(sourceRange)
+      const injectingRangeSemver = extractSemver(injectingRange)
+      const r = tryGetNewerRange(sourceRangeSemver, injectingRangeSemver)
       const didGetNewer = !!r
+
       // if failed to infer newer version, use existing one because it's likely
       // built-in
-      res[name] = didGetNewer ? injectSemver(r2, r) : r1
+      result[depName] = didGetNewer
+        ? injectSemver(injectingRange, r)
+        : sourceRange
+
       // if changed, update source
-      if (res[name] === r2) {
-        sources[name] = generatorId
+      if (result[depName] === injectingRange) {
+        sources[depName] = generatorId
       }
+
       // warn incompatible version requirements
       if (
-        !forceNewVersion &&
-        (
-          !semver.validRange(r1semver) ||
-          !semver.validRange(r2semver) ||
-          !semver.intersects(r1semver, r2semver)
-        )
+        warnIncompatibleVersions &&
+        (!semver.validRange(sourceRangeSemver) ||
+          !semver.validRange(injectingRangeSemver) ||
+          !semver.intersects(sourceRangeSemver, injectingRangeSemver))
       ) {
         warn(
-          `conflicting versions for project dependency "${name}":\n\n` +
-          `- ${r1} injected by generator "${sourceGeneratorId}"\n` +
-          `- ${r2} injected by generator "${generatorId}"\n\n` +
-          `Using ${didGetNewer ? `newer ` : ``}version (${res[name]}), but this may cause build errors.`
+          `conflicting versions for project dependency "${depName}":\n\n` +
+            `- ${sourceRange} injected by generator "${sourceGeneratorId}"\n` +
+            `- ${injectingRange} injected by generator "${generatorId}"\n\n` +
+            `Using ${didGetNewer ? `newer ` : ``}version (${
+              result[depName]
+            }), but this may cause build errors.`
         )
       }
     }
   }
-  return res
+  return result
 }