A motor control system includes a voltage regulating module, an auxiliary activating module, and a drive module. The voltage regulating module is operable to receive a voltage and generate an electrical level regulated voltage by regulating the voltage. The auxiliary activating module is operable to generate a constant duty cycle signal and output the constant duty cycle signal for a period. The drive module is operable to receive the electrical level regulated voltage and the constant duty cycle signal, and control a motor based on the electrical level regulated voltage and the constant duty signal. Also, the present invention also discloses a fan which is applied to the above-mentioned motor control system.