The invention provides a motor controller arousal system fault handling method and a motor controller. The method comprises the steps that when the motor controller confirms that an arousal signal isabnormal, whether the current communication state with the whole vehicle controller is normal or not is judged; if not, a motor is controlled to stop torque outputting after warning information is output. In this way, fault handling of a motor controller arousal system is achieved when the arousal signal is abnormal, and the phenomenon that when the arousal signal is abnormal, serious damage is caused to the driving safety when power down operation is directly executed by the motor controller is avoided, the driving safety is improved, and the user experience is improved.