Hydrogen fuel cell as a very potential direction, it not only has the characteristics of high electrical efficiency, low operating temperature and environmental friendliness, but also has a wide range of applications in the field of transportation and mobile power equipment. This paper considers that PEMFC has better working efficiency when operating in the optimal temperature range, which also has an important impact on the life and performance of PEMFC. Therefore, the control strategy of PEMFC thermal management system is studied. The parameters of PEMFC components are analyzed, the thermal management system is designed, the thermal management model is built, and the model is connected with the reactor model. The PI controller of the PEMFC thermal management system is designed to regulate the inlet cooling water temperature of the reactor and adjust the working temperature of the reactor. Due to the poor dynamic performance of PI control, a fractional-order PI controller based on snake optimization is proposed for heat sink control, aiming to improve the system’s control effectiveness. The simulation results show that the maximum overshoot is reduced by 1.3 Kelvin (K) in the fractional order PI optimized by snake optimization algorithm. Adjustment time is reduced by 24 s.