A motor control system is disclosed. The motor control system includes a level-shifting unit, a motor unit and a control unit. The level-shifting unit receives an original pulse width modulation (PWM) signal to generate an output PWM signal. When a first high level of the original PWM signal is larger than a first reference value, the level-shifting unit shifts a second high level of the output PWM signal to a set high level. When a first low level of the original PWM signal is lower than a second reference value, the level-shifting unit shifts a second low level of the output PWM signal to a set low level. The control unit controls the speed of the motor according to the output PWM signal.