A motor controller comprises a switch circuit and a driving circuit. 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 motor controller utilizes a first pulse width modulation waveform and a second pulse width modulation waveform for driving the three-phase motor, where the first pulse width modulation waveform and the second pulse width modulation waveform have different frequencies from each other. The motor controller utilizes the second pulse width modulation waveform to detect a phase switching time point, where the frequency of the first pulse width modulation waveform is greater than the frequency of the second pulse width modulation waveform.