The performance of the air compressor influences that of the fuel cell system significantly. Therefore, it is urgent to develop a high-performance air compressor for fuel cell vehicles. In this paper, an analytical model of centrifugal compressor performance is established, which can predict the performance of centrifugal compressors under various speeds precisely. Then, the dynamic model of the electric-driven centrifugal compressor system is presented considering rotor dynamics and the dynamic characteristics of the motor. The torque ripple caused by the non-sinusoidal distribution of the permanent magnet field is considered. Based on experiment results, the output performance of the fuel cell stack is modeled. Finally, the influence of motor torque ripple on the performance of centrifugal compressor and fuel cell system is analyzed through simulations. The results show that torque ripple causes lower speed oscillation under high speeds so that it has little effect on the output performance of the centrifugal compressor. Therefore, in the case of matching the operating conditions of the centrifugal compressor and the fuel cell stack, the low-speed operation time of the centrifugal compressor should be reduced. For the electric-driven centrifugal compressors, whose long-running operations are medium-high speed conditions, torque ripple is not the main consideration in the motor selection or design, and the switched reluctance motor is a good choice. Moreover, contrary to intuition, the motor torque ripple can improve the stability of the compression system. This study can guide the design of high-performance centrifugal compressors for fuel cell vehicles.