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Control design is important for proton exchange membrane fuel cell (PEMFC) generator. This work researched the anode system of a 60-kW PEMFC generator. Both anode pressure and humidity must he maintained at ideal levels during steady operation. In view of characteristics and requirements of the system, a hybrid intelligent PID controller is designed specifically based on dynamic simulation. A single neuron PI controller is used for anode humidity by adjusting the water injection to the hydrogen cell. Another incremental PID controller, based on the diagonal recurrent neural network (DRNN) dynamic identification, is used to control anode pressure to be more stable and exact by adjusting the hydrogen flow rate. This control strategy can avoid the coupling problem of the PEMFC and achieve a more adaptive ability. Simulation results showed that the control strategy can maintain both anode humidity and pressure at ideal levels regardless of variable load, nonlinear dynamic and coupling characteristics of the system. This work will give some guides for further control design and applications of the total PEMFC generator.