The present invention provides a motor control system and method thereof. The motor control system comprises a motor controller and a compensation device. The motor controller is used for generating a motor control output according to a reference signal and a first signal. The compensation device is used for generating a compensated motor control output according to the motor control output and a second signal. Moreover, the compensation device utilizes the compensated motor control output to reduce the steady-state phase error between the first signal and the reference signal.