diff --git a/store/migrator.go b/store/migrator.go
index 920bfe5157aa8..e3ddfadab3508 100644
--- a/store/migrator.go
+++ b/store/migrator.go
@@ -35,7 +35,8 @@ const (
 
 // Migrate applies the latest schema to the database.
 func (s *Store) Migrate(ctx context.Context) error {
-	if err := s.preMigrate(ctx); err != nil {
+	isFirstMigration, err := s.preMigrate(ctx)
+	if err != nil {
 		return errors.Wrap(err, "failed to pre-migrate")
 	}
 
@@ -59,7 +60,7 @@ func (s *Store) Migrate(ctx context.Context) error {
 			return errors.Wrap(err, "failed to get current schema version")
 		}
 
-		if version.IsVersionGreaterThan(schemaVersion, latestMigrationHistoryVersion) {
+		if isFirstMigration || version.IsVersionGreaterThan(schemaVersion, latestMigrationHistoryVersion) {
 			filePaths, err := fs.Glob(migrationFS, fmt.Sprintf("%s*/*.sql", s.getMigrationBasePath()))
 			if err != nil {
 				return errors.Wrap(err, "failed to read migration files")
@@ -79,7 +80,7 @@ func (s *Store) Migrate(ctx context.Context) error {
 				if err != nil {
 					return errors.Wrap(err, "failed to get schema version of migrate script")
 				}
-				if version.IsVersionGreaterThan(fileSchemaVersion, latestMigrationHistoryVersion) && version.IsVersionGreaterOrEqualThan(schemaVersion, fileSchemaVersion) {
+				if version.IsVersionGreaterOrEqualThan(fileSchemaVersion, latestMigrationHistoryVersion) && version.IsVersionGreaterOrEqualThan(schemaVersion, fileSchemaVersion) {
 					bytes, err := migrationFS.ReadFile(filePath)
 					if err != nil {
 						return errors.Wrapf(err, "failed to read minor version migration file: %s", filePath)
@@ -116,53 +117,55 @@ func (s *Store) Migrate(ctx context.Context) error {
 	return nil
 }
 
-func (s *Store) preMigrate(ctx context.Context) error {
+func (s *Store) preMigrate(ctx context.Context) (isFirstMigration bool, err error) {
 	// TODO: using schema version in basic setting instead of migration history.
 	migrationHistoryList, err := s.driver.FindMigrationHistoryList(ctx, &FindMigrationHistory{})
 	// If any error occurs or no migration history found, apply the latest schema.
 	if err != nil || len(migrationHistoryList) == 0 {
+		isFirstMigration = true
+
 		if err != nil {
 			slog.Warn("failed to find migration history in pre-migrate", slog.String("error", err.Error()))
 		}
 		filePath := s.getMigrationBasePath() + LatestSchemaFileName
 		bytes, err := migrationFS.ReadFile(filePath)
 		if err != nil {
-			return errors.Errorf("failed to read latest schema file: %s", err)
+			return isFirstMigration, errors.Errorf("failed to read latest schema file: %s", err)
 		}
 		schemaVersion, err := s.GetCurrentSchemaVersion()
 		if err != nil {
-			return errors.Wrap(err, "failed to get current schema version")
+			return isFirstMigration, errors.Wrap(err, "failed to get current schema version")
 		}
 
 		// Start a transaction to apply the latest schema.
 		tx, err := s.driver.GetDB().Begin()
 		if err != nil {
-			return errors.Wrap(err, "failed to start transaction")
+			return isFirstMigration, errors.Wrap(err, "failed to start transaction")
 		}
 		defer tx.Rollback()
 		if err := s.execute(ctx, tx, string(bytes)); err != nil {
-			return errors.Errorf("failed to execute SQL file %s, err %s", filePath, err)
+			return isFirstMigration, errors.Errorf("failed to execute SQL file %s, err %s", filePath, err)
 		}
 		if err := tx.Commit(); err != nil {
-			return errors.Wrap(err, "failed to commit transaction")
+			return isFirstMigration, errors.Wrap(err, "failed to commit transaction")
 		}
 
 		// TODO: using schema version in basic setting instead of migration history.
 		if _, err := s.driver.UpsertMigrationHistory(ctx, &UpsertMigrationHistory{
 			Version: schemaVersion,
 		}); err != nil {
-			return errors.Wrap(err, "failed to upsert migration history")
+			return isFirstMigration, errors.Wrap(err, "failed to upsert migration history")
 		}
 		if err := s.updateCurrentSchemaVersion(ctx, schemaVersion); err != nil {
-			return errors.Wrap(err, "failed to update current schema version")
+			return isFirstMigration, errors.Wrap(err, "failed to update current schema version")
 		}
 	}
 	if s.Profile.Mode == "prod" {
 		if err := s.normalizedMigrationHistoryList(ctx); err != nil {
-			return errors.Wrap(err, "failed to normalize migration history list")
+			return isFirstMigration, errors.Wrap(err, "failed to normalize migration history list")
 		}
 	}
-	return nil
+	return isFirstMigration, nil
 }
 
 func (s *Store) getMigrationBasePath() string {