A motor controller comprises a switch circuit and a control unit. The switch circuit is coupled to a motor for driving the motor. The control unit generates a control signal to control the switch circuit. The motor controller determines a non-excitation time. When the motor is in a locked state, the motor controller enables the non-excitation time to be a variable value. The motor controller utilizes the non-excitation time to achieve a lock protection function. The motor controller determines whether the motor is in the locked state by detecting a rotor speed or a rotor temperature. Moreover, the motor controller further comprises a driving signal, where the driving signal has the non-excitation time.