The liquid cooling system (LCS) of the proton exchange membrane (PEM) fuel cell suffers from large time delay, coupling, uncertainties, and various disturbances, making it susceptible to temperature regulation overshoot and control oscillation. This article focuses on a composite control scheme for the LCS that has effectively addressed the aforementioned issues. We first propose a two-layer control approach for the pump to minimize coupling, and an average delay model (ADM) for radiator whose parameter uncertainties are removed by equilibrium optimizer (EO). To overcome disturbances, an adaptive sliding mode control (ASMC) based on extended state observer (ESO) is presented, and its finite-time convergence is demonstrated. Additionally, the indirect regulation for the stack temperature is designed to considerably reduce the time delay in the fan control loop. Co-simulation results indicate that the proposed ASMC significantly suppresses the chattering phenomenon compared with regular sliding mode control (SMC). In contrast to incremental fuzzy control, the proposed scheme possesses superiorities in response speed, tracking accuracy, anti-disturbance, as well as suppression of overshoot and oscillation.