An improved temperature control strategy by variation of air inlet pressure was proposed to solve the strong coupling problem that exists in the process of actual operation of a proton exchange membrane fuel cell (PEMFC) and to avoid the occurrence of instantaneous high temperature in the internal stack during a large amplitude. In order to adjust the cooling water inlet pressure, this strategy controls the velocity of cooling water by adjusting the speed of cooling water pump, and controls the inlet temperature of cooling water by regulating the rotational speed of the radiator fan. Taking into account the pressure-withstanding ability of stack plates, comparative experiments between the traditional control strategy and the improved control strategy were made on a self-developed multifunctional PEMFC test platform. The results show that the improved temperature control strategy could reduce the maximum overshoot of the cooling water inlet temperature by 34.7% and decrease the maximum difference between the cooling water inlet and outlet temperatures by 17.8%. Consequently, a higher control precision was achieved, and the response speed of system was improved with a maximum time reduction of more than 100 s when the current is reduced from 120 A to 90 A. Therefore, this strategy can meet the requirements on the temperature control of fuel cell systems.