A universal series bus (USB) frequency synchronous apparatus using a start of frame (SOF) signal generated by a master device to mark a reference interval is disclosed. The frequency synchronizing apparatus includes a frequency divider, a counter unit with a default pulse number, an arithmetic unit, and an adjusting unit. The frequency divider divides a high frequency signal by a variable frequency factor to generate a lock frequency signal. The counter is used to detect a pulse number of the lock frequency signal at a reference interval and obtain a pulse difference between the default pulse number and the detected pulse number of the lock frequency signal.