diff --git a/backend/core/models/migrationscripts/20240603_add_pull_request_id_index_for_pr_comments_table.go b/backend/core/models/migrationscripts/20240603_add_pull_request_id_index_for_pr_comments_table.go
new file mode 100644
index 00000000000..9e6d7b6edc9
--- /dev/null
+++ b/backend/core/models/migrationscripts/20240603_add_pull_request_id_index_for_pr_comments_table.go
@@ -0,0 +1,46 @@
+/*
+Licensed to the Apache Software Foundation (ASF) under one or more
+contributor license agreements.  See the NOTICE file distributed with
+this work for additional information regarding copyright ownership.
+The ASF licenses this file to You under the Apache License, Version 2.0
+(the "License"); you may not use this file except in compliance with
+the License.  You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+package migrationscripts
+
+import (
+	"github.com/apache/incubator-devlake/core/context"
+	"github.com/apache/incubator-devlake/core/errors"
+	"github.com/apache/incubator-devlake/helpers/migrationhelper"
+)
+
+type addPullRequestIdIndexToPullRequestComments struct{}
+
+type pullRequestComments20240602 struct {
+	PullRequestId string `gorm:"index"`
+}
+
+func (pullRequestComments20240602) TableName() string {
+	return "pull_request_comments"
+}
+
+func (u *addPullRequestIdIndexToPullRequestComments) Up(basicRes context.BasicRes) errors.Error {
+	return migrationhelper.AutoMigrateTables(basicRes, &pullRequestComments20240602{})
+}
+
+func (*addPullRequestIdIndexToPullRequestComments) Version() uint64 {
+	return 20240602103401
+}
+
+func (*addPullRequestIdIndexToPullRequestComments) Name() string {
+	return "add pull_request_id index for pull_request_comments"
+}
diff --git a/backend/core/models/migrationscripts/20240603_add_pull_request_id_index_for_pr_commits_table.go b/backend/core/models/migrationscripts/20240603_add_pull_request_id_index_for_pr_commits_table.go
new file mode 100644
index 00000000000..ddf381edcd2
--- /dev/null
+++ b/backend/core/models/migrationscripts/20240603_add_pull_request_id_index_for_pr_commits_table.go
@@ -0,0 +1,72 @@
+/*
+Licensed to the Apache Software Foundation (ASF) under one or more
+contributor license agreements.  See the NOTICE file distributed with
+this work for additional information regarding copyright ownership.
+The ASF licenses this file to You under the Apache License, Version 2.0
+(the "License"); you may not use this file except in compliance with
+the License.  You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+package migrationscripts
+
+import (
+	"github.com/apache/incubator-devlake/core/context"
+	"github.com/apache/incubator-devlake/core/errors"
+	"net/url"
+	"strings"
+)
+
+type addPullRequestIdIndexToPullRequestCommits struct{}
+
+func (*addPullRequestIdIndexToPullRequestCommits) Up(basicRes context.BasicRes) errors.Error {
+	dbUrl := basicRes.GetConfig("DB_URL")
+	if dbUrl == "" {
+		return errors.BadInput.New("DB_URL is required")
+	}
+	u, err1 := url.Parse(dbUrl)
+	if err1 != nil {
+		return errors.Convert(err1)
+	}
+	switch strings.ToLower(u.Scheme) {
+	case "mysql":
+		db := basicRes.GetDal()
+		err := db.Exec("ALTER TABLE pull_request_commits DROP PRIMARY KEY;")
+		if err != nil {
+			return err
+		}
+		err = db.Exec("ALTER TABLE pull_request_commits ADD PRIMARY KEY (pull_request_id, commit_sha);")
+		if err != nil {
+			return err
+		}
+		return nil
+	case "postgresql", "postgres", "pg":
+		db := basicRes.GetDal()
+		err := db.Exec("ALTER TABLE pull_request_commits DROP CONSTRAINT pull_request_commits_pkey;")
+		if err != nil {
+			return err
+		}
+		err = db.Exec("ALTER TABLE pull_request_commits ADD PRIMARY KEY (pull_request_id, commit_sha);")
+		if err != nil {
+			return err
+		}
+		return nil
+	default:
+		return nil
+	}
+}
+
+func (*addPullRequestIdIndexToPullRequestCommits) Version() uint64 {
+	return 20240602103400
+}
+
+func (*addPullRequestIdIndexToPullRequestCommits) Name() string {
+	return "changing pull_request_commits primary key columns order"
+}
diff --git a/backend/core/models/migrationscripts/register.go b/backend/core/models/migrationscripts/register.go
index 53e2218c14f..55d67a1b29f 100644
--- a/backend/core/models/migrationscripts/register.go
+++ b/backend/core/models/migrationscripts/register.go
@@ -123,5 +123,7 @@ func All() []plugin.MigrationScript {
 		new(modifyPrAssigneeAndReviewerId),
 		new(addChangesToPr),
 		new(addMergedByToPr),
+		new(addPullRequestIdIndexToPullRequestCommits),
+		new(addPullRequestIdIndexToPullRequestComments),
 	}
 }