The thermal management of proton exchange membrane fuel cells (PEMFCs) influences the safety, durability, and operating efficiency of hydrogen fuel cell vehicles. A thermal management control method is proposed for PEMFCs in this research to maintain the temperature at the inlet and outlet of the stack at the set values. A two-dimensional fuzzy controller is designed based on the temperature changes at the inlet and outlet of the stack in the thermal management system model of PEMFCs, where the membership function of the fuzzy controller is optimized by using the genetic algorithm, so that the control precision of the fuzzy controller is higher. A hydrogen fuel cell vehicle from the Autonomie software is used to validate the proposed thermal management method of the PEMFC on two standard vehicle driving conditions. Simulation results show that the fuzzy controller optimized by the genetic algorithm presents the higher control accuracy than the one without the optimization.