diff --git a/packages/vite/src/node/__tests__/config.spec.ts b/packages/vite/src/node/__tests__/config.spec.ts
index 19ec294d0..ead5927e4 100644
--- a/packages/vite/src/node/__tests__/config.spec.ts
+++ b/packages/vite/src/node/__tests__/config.spec.ts
@@ -1750,6 +1750,18 @@ describe('loadConfigFromFile', () => {
       expect(await loadWithWarnings('clean')).toHaveLength(0)
     })
 
+    test('does not warn for an .mts config under a CommonJS package', async () => {
+      const cwd = process.cwd()
+      process.chdir(path.resolve(compatRoot, 'mts-config'))
+      try {
+        expect(
+          await loadWithWarnings('mts-config', 'vite.config.mts'),
+        ).toHaveLength(0)
+      } finally {
+        process.chdir(cwd)
+      }
+    })
+
     test('does not warn for a CJS config using __dirname', async () => {
       expect(await loadWithWarnings('cjs', 'vite.config.cjs')).toHaveLength(0)
     })
diff --git a/packages/vite/src/node/__tests__/fixtures/config/native-compat/mts-config/package.json b/packages/vite/src/node/__tests__/fixtures/config/native-compat/mts-config/package.json
new file mode 100644
index 000000000..88f8d5b1f
--- /dev/null
+++ b/packages/vite/src/node/__tests__/fixtures/config/native-compat/mts-config/package.json
@@ -0,0 +1,5 @@
+{
+  "name": "@vitejs/test-native-compat-mts",
+  "type": "commonjs",
+  "private": true
+}
diff --git a/packages/vite/src/node/__tests__/fixtures/config/native-compat/mts-config/vite.config.mts b/packages/vite/src/node/__tests__/fixtures/config/native-compat/mts-config/vite.config.mts
new file mode 100644
index 000000000..4f1b25a0c
--- /dev/null
+++ b/packages/vite/src/node/__tests__/fixtures/config/native-compat/mts-config/vite.config.mts
@@ -0,0 +1,3 @@
+import { defineConfig } from 'vite'
+
+export default defineConfig({})
diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml
index 58e303106..763efb7c5 100644
--- a/pnpm-lock.yaml
+++ b/pnpm-lock.yaml
@@ -459,6 +459,8 @@ importers:
 
   packages/vite/src/node/__tests__/fixtures/config/native-compat/esm-in-commonjs-pkg: {}
 
+  packages/vite/src/node/__tests__/fixtures/config/native-compat/mts-config: {}
+
   packages/vite/src/node/__tests__/fixtures/config/native-import: {}
 
   packages/vite/src/node/__tests__/fixtures/config/plugin-module-condition: {}