diff --git a/e2e/projects/fixtures/packages/client/rstest.config.ts b/e2e/projects/fixtures/packages/client/rstest.config.ts
index 379b67d2e..30351a3c2 100644
--- a/e2e/projects/fixtures/packages/client/rstest.config.ts
+++ b/e2e/projects/fixtures/packages/client/rstest.config.ts
@@ -4,6 +4,7 @@ import rsbuildConfig from './rsbuild.config';
 export default defineProject({
   projects: [
     {
+      root: __dirname,
       ...(rsbuildConfig as RstestConfig),
       name: 'client-jsdom',
       testEnvironment: 'jsdom',
@@ -11,6 +12,7 @@ export default defineProject({
       exclude: ['test/node.test.ts'],
     },
     {
+      root: __dirname,
       name: 'client-node',
       include: ['test/node.test.ts'],
     },
diff --git a/e2e/projects/index.test.ts b/e2e/projects/index.test.ts
index 937a8ab75..7475adc0c 100644
--- a/e2e/projects/index.test.ts
+++ b/e2e/projects/index.test.ts
@@ -51,6 +51,33 @@ describe('test projects', () => {
     }, 15_000);
   });
 
+  it('should run project correctly with specified config root', async () => {
+    const { cli, expectExecSuccess } = await runRstestCli({
+      command: 'rstest',
+      args: ['run', '--globals', '-c', 'packages/client/rstest.config.ts'],
+      options: {
+        nodeOptions: {
+          cwd: join(__dirname, 'fixtures'),
+        },
+      },
+    });
+
+    await expectExecSuccess();
+    const logs = cli.stdout.split('\n').filter(Boolean);
+
+    // test log print
+    // should only run client project
+    expect(
+      logs.find((log) => log.includes('packages/node/test/index.test.ts')),
+    ).toBeFalsy();
+    expect(
+      logs.find((log) => log.includes('packages/client/test/App.test.tsx')),
+    ).toBeTruthy();
+    expect(
+      logs.find((log) => log.includes('packages/client/test/node.test.ts')),
+    ).toBeTruthy();
+  });
+
   it('should run projects fail when project not found', async () => {
     const { expectExecFailed, expectStderrLog } = await runRstestCli({
       command: 'rstest',
diff --git a/examples/node/rstest.config.ts b/examples/node/rstest.config.ts
index 9ee3cbabc..af9f402ec 100644
--- a/examples/node/rstest.config.ts
+++ b/examples/node/rstest.config.ts
@@ -1,3 +1,5 @@
 import { defineConfig } from '@rstest/core';
 
-export default defineConfig({});
+export default defineConfig({
+  root: __dirname,
+});
diff --git a/packages/core/src/cli/init.ts b/packages/core/src/cli/init.ts
index 48ba8314e..0ee61ee34 100644
--- a/packages/core/src/cli/init.ts
+++ b/packages/core/src/cli/init.ts
@@ -104,19 +104,25 @@ function mergeWithCLIOptions(
 }
 
 async function resolveConfig(
-  options: CommonOptions & Required<Pick<CommonOptions, 'root'>>,
+  options: CommonOptions & { cwd: string },
 ): Promise<{
   config: RstestConfig;
   configFilePath?: string;
 }> {
   const { content: config, filePath: configFilePath } = await loadConfig({
-    cwd: options.root,
+    cwd: options.cwd,
     path: options.config,
     configLoader: options.configLoader,
   });
 
+  const mergedConfig = mergeWithCLIOptions(config, options);
+
+  if (!mergedConfig.root) {
+    mergedConfig.root = options.cwd;
+  }
+
   return {
-    config: mergeWithCLIOptions(config, options),
+    config: mergedConfig,
     configFilePath: configFilePath ?? undefined,
   };
 }
@@ -219,7 +225,7 @@ export async function resolveProjects({
         const { config, configFilePath } = await resolveConfig({
           ...options,
           config: isDirectory ? undefined : project,
-          root: projectRoot,
+          cwd: projectRoot,
         });
 
         if (configFilePath) {
@@ -290,7 +296,7 @@ export async function initCli(options: CommonOptions): Promise<{
 
   const { config, configFilePath } = await resolveConfig({
     ...options,
-    root,
+    cwd: options.root ? getAbsolutePath(cwd, options.root) : cwd,
   });
 
   const projects = await resolveProjects({ config, root, options });