In order to make hybrid electric vehicles with good fuel economy, frequent starting and stopping of the engine is inevitable. Specifically, torque ripple caused by the engine auto-start and stop can transfer to the driver seat through the vehicle body structure, and effect the quality of the ride. In addition to that, the electric motor’s rapid reaction can also increase the driveline vibration. This paper presents a car motor control system to reduce these vibrations. The motor control system controls the electric motor to compensate the torque ripple caused by the engine during auto-start. This motor control strategy is applied in the Toyota PRIUS motor controller simulation, and greatly improves the ride comfort by 60.2%.