diff --git a/pkg/cluster/operation/destroy.go b/pkg/cluster/operation/destroy.go
index 08e53b9e8d..49985942d5 100644
--- a/pkg/cluster/operation/destroy.go
+++ b/pkg/cluster/operation/destroy.go
@@ -382,6 +382,15 @@ func DestroyComponent(ctx context.Context, instances []spec.Instance, cls spec.T
 			}
 		}
 
+		// For TiKV, we need to delete all extra data directories if the data is not retained.
+		if ins.ComponentName() == spec.ComponentTiKV {
+			for _, dir := range ins.UsedDirs() {
+				if !dataRetained {
+					delPaths.Insert(dir)
+				}
+			}
+		}
+
 		// For TiFlash, we need to delete storage.remote.cache.dir
 		if ins.ComponentName() == spec.ComponentTiFlash {
 			tiflashInstance := ins.(*spec.TiFlashInstance)
diff --git a/pkg/cluster/spec/parse_topology_test.go b/pkg/cluster/spec/parse_topology_test.go
index 4b544da329..b880325bfb 100644
--- a/pkg/cluster/spec/parse_topology_test.go
+++ b/pkg/cluster/spec/parse_topology_test.go
@@ -17,6 +17,7 @@ import (
 	"fmt"
 	"os"
 	"path/filepath"
+	"sort"
 	"testing"
 
 	"github.com/pingcap/check"
@@ -277,6 +278,51 @@ tikv_servers:
 	})
 }
 
+func (s *topoSuite) TestTiKVServerConfigs(c *check.C) {
+	// test tikv server config section
+	withTempFile(`
+global:
+  user: tidb
+  deploy_dir: my-global-deploy
+  data_dir: my-global-data
+  log_dir: my-global-log
+
+server_configs:
+  tikv:
+    storage.reserve-space: 1K
+    storage.data-dir: /data1/tikv
+    raft-engine:
+      dir: /data1/data/raft
+      spill-dir: /data1/data/spill
+    rocksdb.wal-dir: /data2/data/wal
+    rocksdb.titan.dirname: /data2/data/titan
+
+tikv_servers:
+  - host: 172.16.5.140
+    port: 20161
+    status_port: 20181
+`, func(file string) {
+		topo := Specification{}
+		err := ParseTopologyYaml(file, &topo)
+		c.Assert(err, check.IsNil)
+		ExpandRelativeDir(&topo)
+
+		c.Assert(topo.TiKVServers[0].DeployDir, check.Equals, "/home/tidb/my-global-deploy/tikv-20161")
+		c.Assert(topo.TiKVServers[0].DataDir, check.Equals, "/home/tidb/my-global-deploy/tikv-20161/my-global-data")
+		c.Assert(topo.TiKVServers[0].LogDir, check.Equals, "/home/tidb/my-global-deploy/tikv-20161/my-global-log")
+
+		c.Assert(topo.ServerConfigs.TiKV["storage.data-dir"], check.Equals, "/data1/tikv")
+		c.Assert(topo.ServerConfigs.TiKV["rocksdb.wal-dir"], check.Equals, "/data2/data/wal")
+		c.Assert(topo.ServerConfigs.TiKV["rocksdb.titan.dirname"], check.Equals, "/data2/data/titan")
+
+		extraDirs := topo.TiKVServers[0].getExtraDeployDirs(topo.ServerConfigs.TiKV)
+		sort.Strings(extraDirs)
+		targetDirs := []string{"/data1/tikv", "/data1/data/raft", "/data1/data/spill", "/data2/data/wal", "/data2/data/titan"}
+		sort.Strings(targetDirs)
+		c.Assert(extraDirs, check.DeepEquals, targetDirs)
+	})
+}
+
 func (s *topoSuite) TestTiFlashStorage(c *check.C) {
 	// test tiflash storage section, 'storage.main.dir' should not be defined in server_configs
 	withTempFile(`
diff --git a/pkg/cluster/spec/tikv.go b/pkg/cluster/spec/tikv.go
index 4c40fb1408..fbb58019a9 100644
--- a/pkg/cluster/spec/tikv.go
+++ b/pkg/cluster/spec/tikv.go
@@ -164,6 +164,80 @@ func (s *TiKVSpec) Labels() (map[string]string, error) {
 	return lbs, nil
 }
 
+// getExtraDeployDirs returns the extra directories that needs to be checked.
+func (s *TiKVSpec) getExtraDeployDirs(globalConf map[string]any) []string {
+	// Extract the directory from the configuration.
+	var extractDir = func(dir any, rootPath string) string {
+		realDir := strings.TrimSpace(dir.(string))
+		// Skip the relative path under the root path.
+		if realDir == "" || (strings.HasPrefix(realDir, "./") || strings.HasPrefix(realDir, rootPath)) {
+			return ""
+		}
+		elemStr := strings.TrimSuffix(realDir, "/")
+		return elemStr
+	}
+	// Search the directory from the nested configuration.
+	var searchDir = func(fieldName string, confs map[string]any) string {
+		if confs == nil {
+			return ""
+		}
+		steps := strings.Split(fieldName, ".")
+		if len(steps) == 0 {
+			return ""
+		}
+		// Search the directory from the nested configuration.
+		var tmpConfs map[any]any
+		for _, step := range steps {
+			if step == steps[0] {
+				tmpConfs, _ = confs[steps[0]].(map[any]any)
+				if tmpConfs == nil {
+					return ""
+				}
+				continue
+			}
+			nextTmpConfs, ok := tmpConfs[step].(map[any]any)
+			if !ok || nextTmpConfs == nil {
+				break
+			}
+			tmpConfs = nextTmpConfs
+		}
+		dir, ok := tmpConfs[steps[len(steps)-1]]
+		if !ok {
+			return ""
+		}
+		return strings.TrimSpace(dir.(string))
+	}
+
+	extraDirs := []string{}
+	rootPath := s.DataDir
+	candidates := []string{
+		"storage.data-dir",
+		"rocksdb.wal-dir",
+		"rocksdb.titan.dirname",
+		"raft-engine.dir",
+		"raft-engine.spill-dir",
+	}
+	for _, candidate := range candidates {
+		// Check the global configurations and the instance configurations.
+		for _, conf := range []any{globalConf, s.Config} {
+			config := conf.(map[string]any)
+			dir, ok := config[candidate]
+			if ok {
+				elemStr := extractDir(dir, rootPath)
+				if elemStr != "" {
+					extraDirs = append(extraDirs, elemStr)
+				}
+			}
+			// Check the configuration with nested fields.
+			dataDir := searchDir(candidate, config)
+			if dataDir != "" {
+				extraDirs = append(extraDirs, dataDir)
+			}
+		}
+	}
+	return extraDirs
+}
+
 // TiKVComponent represents TiKV component.
 type TiKVComponent struct{ Topology *Specification }
 
@@ -205,6 +279,8 @@ func (c *TiKVComponent) Instances() []Instance {
 	ins := make([]Instance, 0, len(c.Topology.TiKVServers))
 	for _, s := range c.Topology.TiKVServers {
 		s := s
+		dirs := []string{s.DeployDir, s.DataDir}
+		dirs = append(dirs, s.getExtraDeployDirs(c.Topology.ServerConfigs.TiKV)...)
 		ins = append(ins, &TiKVInstance{BaseInstance{
 			InstanceSpec: s,
 			Name:         c.Name(),
@@ -221,10 +297,7 @@ func (c *TiKVComponent) Instances() []Instance {
 				s.Port,
 				s.StatusPort,
 			},
-			Dirs: []string{
-				s.DeployDir,
-				s.DataDir,
-			},
+			Dirs:     dirs,
 			StatusFn: s.Status,
 			UptimeFn: func(_ context.Context, timeout time.Duration, tlsCfg *tls.Config) time.Duration {
 				return UptimeByHost(s.GetManageHost(), s.StatusPort, timeout, tlsCfg)