diff --git a/.changeset/wise-donuts-remain.md b/.changeset/wise-donuts-remain.md
new file mode 100644
index 000000000000..e4242a268012
--- /dev/null
+++ b/.changeset/wise-donuts-remain.md
@@ -0,0 +1,7 @@
+---
+'@modern-js/builder-webpack-provider': patch
+---
+
+fix(builder): deep-merge lose array items under tools.tschecker
+
+fix(builder): 修复 deep-merge 在 tools.tschecker 中会丢失数组子元素的问题
diff --git a/packages/builder/builder-webpack-provider/package.json b/packages/builder/builder-webpack-provider/package.json
index 216f29700933..b5a9ffd8c826 100644
--- a/packages/builder/builder-webpack-provider/package.json
+++ b/packages/builder/builder-webpack-provider/package.json
@@ -107,8 +107,8 @@
     "react-refresh": "0.14.0",
     "style-loader": "3.3.3",
     "terser-webpack-plugin": "5.3.9",
-    "tsconfig-paths-webpack-plugin": "4.1.0",
     "ts-loader": "9.4.4",
+    "tsconfig-paths-webpack-plugin": "4.1.0",
     "webpack": "^5.88.1",
     "webpack-subresource-integrity": "5.1.0"
   },
@@ -120,9 +120,9 @@
     "@types/caniuse-lite": "^1.0.1",
     "@types/node": "^14",
     "antd": "4",
-    "typescript": "^5",
     "react": "^18",
-    "react-dom": "^18"
+    "react-dom": "^18",
+    "typescript": "^5"
   },
   "sideEffects": false,
   "publishConfig": {
diff --git a/packages/builder/builder-webpack-provider/tests/plugins/__snapshots__/tsChecker.test.ts.snap b/packages/builder/builder-webpack-provider/tests/plugins/__snapshots__/tsChecker.test.ts.snap
index 52c13110e9e4..fe377e3427f3 100644
--- a/packages/builder/builder-webpack-provider/tests/plugins/__snapshots__/tsChecker.test.ts.snap
+++ b/packages/builder/builder-webpack-provider/tests/plugins/__snapshots__/tsChecker.test.ts.snap
@@ -63,3 +63,36 @@ exports[`plugins/tsChecker > should only apply one tsChecker plugin when there i
   {},
 ]
 `;
+
+exports[`plugins/tsChecker > should tschecker.issue.exclude final config merge correctly 1`] = `
+{
+  "plugins": [
+    ForkTsCheckerWebpackPlugin {
+      "options": {
+        "issue": {
+          "exclude": [
+            {
+              "file": "**/*.(spec|test).ts",
+            },
+            {
+              "file": "**/node_modules/**/*",
+            },
+            {
+              "file": "src/**/*.ts",
+            },
+          ],
+        },
+        "logger": {
+          "error": [Function],
+          "log": [Function],
+        },
+        "typescript": {
+          "configFile": "/path/tsconfig.json",
+          "memoryLimit": 8192,
+          "typescriptPath": "<WORKSPACE>/node_modules/<PNPM_INNER>/typescript/lib/typescript.js",
+        },
+      },
+    },
+  ],
+}
+`;
diff --git a/packages/builder/builder-webpack-provider/tests/plugins/tsChecker.test.ts b/packages/builder/builder-webpack-provider/tests/plugins/tsChecker.test.ts
index 9d98009eafba..64a7462f01f7 100644
--- a/packages/builder/builder-webpack-provider/tests/plugins/tsChecker.test.ts
+++ b/packages/builder/builder-webpack-provider/tests/plugins/tsChecker.test.ts
@@ -80,4 +80,22 @@ describe('plugins/tsChecker', () => {
     const configs = await builder.unwrapWebpackConfigs();
     expect(configs).toMatchSnapshot();
   });
+
+  it('should tschecker.issue.exclude final config merge correctly', async () => {
+    const builder = await createStubBuilder({
+      plugins: [builderPluginTsChecker()],
+      context,
+      builderConfig: {
+        tools: {
+          tsChecker: {
+            issue: {
+              exclude: [{ file: './src/**/*.ts' }],
+            },
+          },
+        },
+      },
+    });
+    const config = await builder.unwrapWebpackConfig();
+    expect(config).toMatchSnapshot();
+  });
 });
diff --git a/packages/builder/builder/package.json b/packages/builder/builder/package.json
index 6c5b8561716d..a7e4432ee5da 100644
--- a/packages/builder/builder/package.json
+++ b/packages/builder/builder/package.json
@@ -65,11 +65,12 @@
     "@rsbuild/monorepo-utils": "0.0.7",
     "@svgr/webpack": "8.0.1",
     "@swc/helpers": "0.5.1",
+    "deepmerge": "^4.3.1",
     "jiti": "^1.20.0"
   },
   "devDependencies": {
-    "@modern-js/builder-webpack-provider": "workspace:*",
     "@modern-js/builder-rspack-provider": "workspace:*",
+    "@modern-js/builder-webpack-provider": "workspace:*",
     "@scripts/build": "workspace:*",
     "@scripts/vitest-config": "workspace:*",
     "@types/babel__core": "^7.20.0",
diff --git a/packages/builder/builder/src/plugins/tsChecker.ts b/packages/builder/builder/src/plugins/tsChecker.ts
index de81e76ee826..1564eebc7a19 100644
--- a/packages/builder/builder/src/plugins/tsChecker.ts
+++ b/packages/builder/builder/src/plugins/tsChecker.ts
@@ -1,6 +1,6 @@
 import { DefaultBuilderPlugin } from '@modern-js/builder-shared';
-import { merge as deepMerge } from '@modern-js/utils/lodash';
 import type { BuilderPluginAPI as WebpackBuilderPluginAPI } from '@modern-js/builder-webpack-provider';
+import deepmerge from 'deepmerge';
 
 export const builderPluginTsChecker = (): DefaultBuilderPlugin => {
   return {
@@ -86,7 +86,7 @@ export const builderPluginTsChecker = (): DefaultBuilderPlugin => {
           },
           config.tools.tsChecker,
           undefined,
-          deepMerge,
+          deepmerge,
         );
 
         if (