This paper investigates the control of the air supply system for marine proton exchange membrane fuel cells. A mathematical model of the air supply system is established, and a sliding mode diagonal decoupling controller based on a state observer is proposed. The control effectiveness is validated through experiments and simulations. A decoupling control strategy for the air supply system of marine fuel cells is presented. First, the load input current of the fuel cell system is selected according to the load characteristics of the target vessel, ensuring that the load current meets the power level of the fuel cell system model. Second, the impact of the cathode pressure on the fuel cell system is analyzed. An observer-based measurement method is proposed to address the measurement issue of cathode pressure. On this basis, a decoupling control strategy combining a diagonal decoupling matrix and sliding mode variable structure control theory is proposed. Finally, the effectiveness of the decoupling controller is validated through Matlab/Simulink. The results show the proposed decoupling controller exhibits superior performance to existing controllers with environmental disturbances, continuous time-varying loads, and step loads. The maximum relative error is 2.95%, the average relative error is 0.022%, and the longest adjustment time is 0.5 s. These results indicate that the control performance of the proposed decoupling controller is superior to that of diagonal PI controllers and sliding mode controllers, thereby validating the superiority of the sliding mode decoupling controller. This article provides a useful method for the development and application of control technology for the air supply system of marine fuel cells.