As one of the most promising sustainable energy technologies available today, proton exchange membrane fuel cell (PEMFC) engines are becoming more and more popular in various applications, especially in transportation vehicles. However, the complexity and the severity of the vehicle operating conditions present challenges to control the temperature distribution in single cells and stack, which is an important factor influencing the performance and durability of PEMFC engines. It has been found that regulating the input and output coolant water temperature can improve the temperature distribution. Therefore, the control objective in this paper is regulating the input and output temperature of coolant water at the same time. Firstly, a coupled model of the thermal management system is established based on the physical structure of PEMFC engines. Then, in order to realize the simultaneous control of the inlet and outlet cooling water temperature of the PEMFC stack, a decoupling controller is proposed and its closed-loop stability is proved. Finally, based on the actual PEMFC engine platform, the effectiveness, accuracy and reliability of the proposed decoupling controller are tested. The experimental results show that with the proposed decoupling controller, the inlet and outlet temperatures of the PEMFC stack cooling water can be accurately controlled on-line. The temperature error range is less than 0.2 °C even under the dynamic current load conditions.