A motor controller with a reverse-bias preventing mechanism includes a pre-charging unit, a protection unit, a conversion unit and a control unit. The pre-charging unit receives a power signal through a first electric-conduction path, and converts the power signal into a pre-charging signal according to a control signal. The protection unit receives the power signal through a second electric-conduction path, and determines whether to output the power signal, according to the polarity of the power signal. The conversion unit, coupled to the protection unit, receives the power signal outputted by the protection unit, and converts the power signal into a work voltage. The control unit, coupled to the conversion unit and the pre-charging unit, receives the work voltage to generate the control signal. The current of the power signal flowing through second electric-conduction path is smaller than the current flowing through first electric-conduction path.