Hydrogen fuel cell system is an emerging power generation system with great potential for application in the automotive industry. In this paper, we design a high-power fuel cell system and take the fuel cell system shutdown purge process as a case, firstly, we complete the control strategy development in Simulink environment. Then the I/O resource configuration and model integration were performed based on the rapid control prototype system of dSPACE. Finally, the code was automatically generated and the simulation verification of the control strategy on this rapid control prototype system was implemented. The results show that the fuel cell system can operate stably according to the demanded power and can execute the shutdown purge procedure according to the established control strategy. This development method, which shortens the development cycle, effectively improves the reliability and flexibility of the control strategy development, and has a high value of use.