Electrolysis systems use proportional–integral–derivative (PID) temperature controllers to maintain stack temperatures around set points. However, because of heat transfer delays in electrolysis systems, the manual tuning of PID temperature controllers is time-consuming, and temperature oscillations often occur. This paper focuses on the design of the PID temperature controller for an alkaline electrolysis system to achieve fast and stable temperature control. A thermal dynamic model of an electrolysis system is established in the frequency domain for controller designs. Based on this model, the temperature stability is analysed by the root distribution, and the PID parameters are optimized considering the temperature overshoot and the settling time. The performance of the optimal PID controllers is experimentally verified. Furthermore, the simulation results show that the before-stack temperature should be used as the feedback variable for small lab-scale systems to suppress stack temperature fluctuations, and the after-stack temperature should be used for larger systems to improve the economy. This study helps ensure the temperature stability and control of electrolysis systems.