Proton exchange membrane fuel cell vehicles are an important technology route to achieve carbon neutrality in transportation. In this paper, a system controller was developed for high efficiency and long durability on an integrated 100 kW passenger car fuel cell system. The complete control program is developed in conjunction with Matlab/Simulink and the Motohawk rapid control prototype. Then, the closed-loop control performance of the controller was discussed, represented by the air subsystem. Finally, with the implementation of the FC controller developed, the dynamic performance of the entire system was studied. The results show that the FC system has an excellent potential in terms of net power, system efficiency, and consistency. The maximum efficiency of the system reaches 62%, and the voltage variation coefficient (Cv) is controlled below 1% during dynamic load changes.