This paper addresses the issues of nonlinearity and coupling between anode pressure and cathode pressure in proton exchange membrane fuel cell (PEMFC) gas supply systems. A fuzzy adaptive PI decoupling control strategy with an improved advanced genetic algorithm (AGA) is proposed. This AGA s utilized to optimize the PI parameters offline, and the fuzzy adaptive algorithm s used to adjust the PI parameters dynamically online to achieve the approximate decoupling control of the PEMFC gas supply system. According to the proposed dynamic model, the PEMFC gas supply system with the fuzzy–AGA–PI decoupling control method was simulated for comparison. The simulation results demonstrate that the proposed control system can reduce the pressure difference more efficiently with the classical control method under different load changes.