diff --git a/pkg/sqlreplay/replay/replay.go b/pkg/sqlreplay/replay/replay.go
index 20dbf8426..e3339699c 100644
--- a/pkg/sqlreplay/replay/replay.go
+++ b/pkg/sqlreplay/replay/replay.go
@@ -214,6 +214,7 @@ func (r *replay) readCommands(ctx context.Context) {
 			Dir:              r.cfg.Input,
 			EncryptionKey:    r.cfg.encryptionKey,
 			EncryptionMethod: r.meta.EncryptMethod,
+			CommandStartTime: r.cfg.CommandStartTime,
 		})
 		if err != nil {
 			r.stop(err)
diff --git a/pkg/sqlreplay/store/line.go b/pkg/sqlreplay/store/line.go
index 13a606dea..d9d6f6a84 100644
--- a/pkg/sqlreplay/store/line.go
+++ b/pkg/sqlreplay/store/line.go
@@ -7,6 +7,7 @@ import (
 	"bufio"
 	"fmt"
 	"io"
+	"time"
 
 	"github.com/pingcap/tidb/br/pkg/storage"
 	"github.com/pingcap/tiproxy/pkg/sqlreplay/cmd"
@@ -32,6 +33,8 @@ type ReaderCfg struct {
 	Format           string
 	EncryptionMethod string
 	EncryptionKey    []byte
+	// Reader will skip the files whose end time is before CommandStartTime.
+	CommandStartTime time.Time
 }
 
 var _ cmd.LineReader = (*loader)(nil)
diff --git a/pkg/sqlreplay/store/rotate.go b/pkg/sqlreplay/store/rotate.go
index 42885c756..c911e7aef 100644
--- a/pkg/sqlreplay/store/rotate.go
+++ b/pkg/sqlreplay/store/rotate.go
@@ -169,12 +169,16 @@ func (r *rotateReader) nextReader() error {
 	var minFileName string
 	fileNamePrefix := getFileNamePrefix(r.cfg.Format)
 	parseFunc := getParseFileNameFunc(r.cfg.Format)
+	fileFilter := getFilterFileNameFunc(r.cfg.Format, r.cfg.CommandStartTime)
 	ctx, cancel := context.WithTimeout(context.Background(), opTimeout)
 	err := r.storage.WalkDir(ctx, &storage.WalkOption{},
 		func(name string, size int64) error {
 			if !strings.HasPrefix(name, fileNamePrefix) {
 				return nil
 			}
+			if !fileFilter(name, fileNamePrefix) {
+				return nil
+			}
 			fileIdx := parseFunc(name, fileNamePrefix)
 			if fileIdx == 0 {
 				r.lg.Warn("traffic file name is invalid", zap.String("filename", name), zap.String("format", r.cfg.Format))
@@ -230,11 +234,21 @@ func getFileNamePrefix(format string) string {
 func getParseFileNameFunc(format string) func(string, string) int64 {
 	switch format {
 	case cmd.FormatAuditLogPlugin:
-		return parseFileTime
+		return parseFileTimeToIdx
 	}
 	return parseFileIdx
 }
 
+func getFilterFileNameFunc(format string, commandStartTime time.Time) func(string, string) bool {
+	switch format {
+	case cmd.FormatAuditLogPlugin:
+		return func(name, fileNamePrefix string) bool {
+			return filterFileByTime(name, fileNamePrefix, commandStartTime)
+		}
+	}
+	return func(string, string) bool { return true }
+}
+
 // Parse the file name to get the file index.
 // filename pattern: traffic-1.log.gz
 func parseFileIdx(name, fileNamePrefix string) int64 {
@@ -262,25 +276,44 @@ func parseFileIdx(name, fileNamePrefix string) int64 {
 
 // Parse the file name to get the file timestamp.
 // filename pattern: tidb-audit-2025-09-10T17-01-56.073.log
-func parseFileTime(name, fileNamePrefix string) int64 {
+func parseFileTime(name, fileNamePrefix string) time.Time {
 	if !strings.HasPrefix(name, fileNamePrefix) {
-		return 0
+		return time.Time{}
 	}
 	startIdx := len(fileNamePrefix)
 	if len(name) <= startIdx+len(fileNameSuffix) {
-		return 0
+		return time.Time{}
 	}
 	endIdx := len(name)
 	if strings.HasSuffix(name, fileCompressFormat) {
 		endIdx -= len(fileCompressFormat)
 	}
 	if !strings.HasSuffix(name[:endIdx], fileNameSuffix) {
-		return 0
+		return time.Time{}
 	}
 	endIdx -= len(fileNameSuffix)
 	ts, err := time.Parse(logTimeLayout, name[startIdx:endIdx])
 	if err != nil {
+		return time.Time{}
+	}
+	return ts
+}
+
+func parseFileTimeToIdx(name, fileNamePrefix string) int64 {
+	ts := parseFileTime(name, fileNamePrefix)
+	if ts.IsZero() {
 		return 0
 	}
 	return ts.UnixNano() / 1000000
 }
+
+func filterFileByTime(name, fileNamePrefix string, commandStartTime time.Time) bool {
+	fileTime := parseFileTime(name, fileNamePrefix)
+	if fileTime.IsZero() {
+		return false
+	}
+	// Be careful that the log file name doesn't contain timezone info.
+	// We assume the log file time is the Local time. But anyway we could workaround it by
+	// adjusting the commandStartTime.
+	return fileTime.After(commandStartTime)
+}
diff --git a/pkg/sqlreplay/store/rotate_test.go b/pkg/sqlreplay/store/rotate_test.go
index 217cd0f01..6d7ec7aff 100644
--- a/pkg/sqlreplay/store/rotate_test.go
+++ b/pkg/sqlreplay/store/rotate_test.go
@@ -12,6 +12,7 @@ import (
 	"path/filepath"
 	"strings"
 	"testing"
+	"time"
 
 	"github.com/pingcap/tiproxy/lib/util/logger"
 	"github.com/pingcap/tiproxy/pkg/sqlreplay/cmd"
@@ -140,7 +141,7 @@ func TestParseFileTime(t *testing.T) {
 	}
 
 	for i, test := range tests {
-		idx := parseFileTime(test.fileName, auditFileNamePrefix)
+		idx := parseFileTimeToIdx(test.fileName, auditFileNamePrefix)
 		require.Equal(t, test.fileIdx, idx, "case %d", i)
 	}
 }
@@ -367,3 +368,91 @@ func TestCompressAndEncrypt(t *testing.T) {
 	require.Equal(t, []byte("testtest"), data[:8])
 	require.NoError(t, reader.Close())
 }
+
+func TestFilterFileNameByStartTime(t *testing.T) {
+	commandStartTime, err := time.Parse(logTimeLayout, "2025-09-10T17-01-56.050")
+	require.NoError(t, err)
+	tests := []struct {
+		fileName        string
+		expectToInclude bool
+	}{
+		// Files after start time should be included
+		{
+			fileName:        "tidb-audit-2025-09-10T17-01-56.073.log",
+			expectToInclude: true,
+		},
+		{
+			fileName:        "tidb-audit-2025-09-10T17-01-56.172.log.gz",
+			expectToInclude: true,
+		},
+		{
+			fileName:        "tidb-audit-2025-09-11T10-30-00.500.log",
+			expectToInclude: true,
+		},
+		// Files before or equal to start time should be excluded
+		{
+			fileName:        "tidb-audit-2025-09-10T17-01-55.073.log",
+			expectToInclude: false,
+		},
+		{
+			fileName:        "tidb-audit-2025-09-10T17-01-56.000.log",
+			expectToInclude: false,
+		},
+		// Invalid file names should be excluded
+		{
+			fileName:        "tidb-audit-invalid-timestamp.log",
+			expectToInclude: false,
+		},
+		{
+			fileName:        "traffic-1.log",
+			expectToInclude: false,
+		},
+		{
+			fileName:        "tidb-audit.log",
+			expectToInclude: false,
+		},
+		{
+			fileName:        "tidb-audit-2025-13-40T25-70-70.log",
+			expectToInclude: false,
+		},
+	}
+	expectedFileOrder := []string{
+		"tidb-audit-2025-09-10T17-01-56.073.log",
+		"tidb-audit-2025-09-10T17-01-56.172.log.gz",
+		"tidb-audit-2025-09-11T10-30-00.500.log",
+	}
+	for i, test := range tests {
+		included := filterFileByTime(test.fileName, auditFileNamePrefix, commandStartTime)
+		require.Equal(t, test.expectToInclude, included, "case %d", i)
+	}
+
+	dir := t.TempDir()
+	require.NoError(t, os.RemoveAll(dir))
+	require.NoError(t, os.MkdirAll(dir, 0777))
+	for _, test := range tests {
+		f, err := os.Create(filepath.Join(dir, test.fileName))
+		require.NoError(t, err)
+		if strings.HasSuffix(test.fileName, ".gz") {
+			w := gzip.NewWriter(f)
+			_, err := w.Write([]byte{})
+			require.NoError(t, err)
+			require.NoError(t, w.Close())
+		}
+		require.NoError(t, f.Close())
+	}
+	storage, err := NewStorage(dir)
+	require.NoError(t, err)
+	defer storage.Close()
+	lg, _ := logger.CreateLoggerForTest(t)
+	l, err := newRotateReader(lg, storage, ReaderCfg{Dir: dir, Format: cmd.FormatAuditLogPlugin, CommandStartTime: commandStartTime})
+	require.NoError(t, err)
+	var fileOrder []string
+	for {
+		if err := l.nextReader(); err != nil {
+			require.True(t, errors.Is(err, io.EOF))
+			break
+		}
+		fileOrder = append(fileOrder, l.curFileName)
+	}
+	require.Equal(t, expectedFileOrder, fileOrder)
+}