A motor controller comprises a switch circuit, a driving circuit, a pulse width modulation circuit, and a Hall sensor. The switch circuit is coupled to a three-phase motor for driving the three-phase motor. The driving circuit generates a plurality of control signals to control the switch circuit. The pulse width modulation circuit generates a pulse width modulation signal to the driving circuit. The pulse width modulation signal has a duty cycle. The Hall sensor is coupled to the pulse width modulation circuit for generating a Hall signal. When the duty cycle is less than an alignment duty cycle, the motor controller generates an alignment waveform based on the initial value of the Hall signal. The alignment waveform may be a part of an M-shaped waveform.