diff --git a/Makefile b/Makefile
index ecd4972ddeaa..dac64e3a6f40 100644
--- a/Makefile
+++ b/Makefile
@@ -163,7 +163,6 @@ GOIMAGEBUILD_CORE=$(GOIMAGEBUILDCMD) $(GOFLAGS) ${GOTAGS} --ldflags "-w -s $(COR
 GOBUILDPATH_CORE=$(GOBUILDPATHINCONTAINER)/src/core
 GOBUILDPATH_JOBSERVICE=$(GOBUILDPATHINCONTAINER)/src/jobservice
 GOBUILDPATH_REGISTRYCTL=$(GOBUILDPATHINCONTAINER)/src/registryctl
-GOBUILDPATH_MIGRATEPATCH=$(GOBUILDPATHINCONTAINER)/src/cmd/migrate-patch
 GOBUILDPATH_STANDALONE_DB_MIGRATOR=$(GOBUILDPATHINCONTAINER)/src/cmd/standalone-db-migrator
 GOBUILDPATH_EXPORTER=$(GOBUILDPATHINCONTAINER)/src/cmd/exporter
 GOBUILDMAKEPATH=make
@@ -546,8 +545,6 @@ cleanbinary:
 	if [ -f $(CORE_BINARYPATH)/$(CORE_BINARYNAME) ] ; then rm $(CORE_BINARYPATH)/$(CORE_BINARYNAME) ; fi
 	if [ -f $(JOBSERVICEBINARYPATH)/$(JOBSERVICEBINARYNAME) ] ; then rm $(JOBSERVICEBINARYPATH)/$(JOBSERVICEBINARYNAME) ; fi
 	if [ -f $(REGISTRYCTLBINARYPATH)/$(REGISTRYCTLBINARYNAME) ] ; then rm $(REGISTRYCTLBINARYPATH)/$(REGISTRYCTLBINARYNAME) ; fi
-	if [ -f $(MIGRATEPATCHBINARYPATH)/$(MIGRATEPATCHBINARYNAME) ] ; then rm $(MIGRATEPATCHBINARYPATH)/$(MIGRATEPATCHBINARYNAME) ; fi
-	rm -rf make/photon/*/binary/
 
 cleanbaseimage:
 	@echo "cleaning base image for photon..."
diff --git a/src/cmd/migrate-patch/README.md b/src/cmd/migrate-patch/README.md
deleted file mode 100644
index 9c9b70568f1e..000000000000
--- a/src/cmd/migrate-patch/README.md
+++ /dev/null
@@ -1,6 +0,0 @@
-# Migrate Patch
-This is a simple program to fix the breakage that was introduced by migrate in notary.
-## Usage
-```sh
-patch -database <db_url>
-```
diff --git a/src/cmd/migrate-patch/main.go b/src/cmd/migrate-patch/main.go
deleted file mode 100644
index eb728b3a1120..000000000000
--- a/src/cmd/migrate-patch/main.go
+++ /dev/null
@@ -1,88 +0,0 @@
-// Copyright Project Harbor Authors
-//
-// Licensed 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 main
-
-import (
-	"database/sql"
-	"flag"
-	"log"
-	"strings"
-	"time"
-
-	_ "github.com/jackc/pgx/v4/stdlib" // registry pgx driver
-)
-
-var dbURL string
-
-const pgSQLAlterStmt string = `ALTER TABLE schema_migrations ADD COLUMN "dirty" boolean NOT NULL DEFAULT false`
-const pgSQLCheckColStmt string = `SELECT T1.C1, T2.C2 FROM
-(SELECT COUNT(*) AS C1 FROM information_schema.tables WHERE table_name='schema_migrations') T1,
-(SELECT COUNT(*) AS C2 FROM information_schema.columns WHERE table_name='schema_migrations' and column_name='dirty') T2`
-const pgSQLDelRows string = `DELETE FROM schema_migrations t WHERE t.version < ( SELECT MAX(version) FROM schema_migrations )`
-
-func init() {
-	urlUsage := `The URL to the target database (driver://url).  Currently it only supports postgres`
-	flag.StringVar(&dbURL, "database", "", urlUsage)
-}
-
-func main() {
-	flag.Parse()
-	log.Printf("Updating database.")
-	if !strings.HasPrefix(dbURL, "postgres://") {
-		log.Fatalf("Invalid URL: '%s'\n", dbURL)
-	}
-	db, err := sql.Open("pgx", dbURL)
-	if err != nil {
-		log.Fatalf("Failed to connect to Database, error: %v\n", err)
-	}
-	defer db.Close()
-
-	c := make(chan struct{})
-	go func() {
-		defer close(c)
-
-		err := db.Ping()
-		for ; err != nil; err = db.Ping() {
-			log.Println("Failed to Ping DB, sleep for 1 second.")
-			time.Sleep(1 * time.Second)
-		}
-	}()
-	select {
-	case <-c:
-	case <-time.After(30 * time.Second):
-		log.Fatal("Failed to connect DB after 30 seconds, time out. \n")
-	}
-
-	row := db.QueryRow(pgSQLCheckColStmt)
-	var tblCount, colCount int
-	if err := row.Scan(&tblCount, &colCount); err != nil {
-		log.Fatalf("Failed to check schema_migrations table, error: %v \n", err)
-	}
-	if tblCount == 0 {
-		log.Println("schema_migrations table does not exist, skip.")
-		return
-	}
-	if colCount > 0 {
-		log.Println("schema_migrations table does not require update, skip.")
-		return
-	}
-	if _, err := db.Exec(pgSQLDelRows); err != nil {
-		log.Fatalf("Failed to clean up table, error: %v", err)
-	}
-	if _, err := db.Exec(pgSQLAlterStmt); err != nil {
-		log.Fatalf("Failed to update database, error: %v \n", err)
-	}
-	log.Println("Done updating database.")
-}