Control design is important for PEMFC (proton exchange membrane fuel cell) distributed power generator to satisfy user requirement for safe and stable operation. For a complex multi-variable dynamic system, a dynamic simulation model is first established. In view of close coupling and non-linear relationships between variables, the intelligent auto-adapted PI decoupling control method is used. From the simulation results it is found that, by bringing quadratic performance index in the single neuron, constructing adaptive PI controller, and adjusting gas flow rates through the second pressure relief valve and air compressor coordinately, both anode and cathode pressures can be maintained at ideal levels. Control design is important for PEMFC (proton exchange membrane fuel cell) distributed power generator to satisfy user requirement for safe and stable operation. For a complex multi-variable dynamic system, a dynamic simulation model is first established. In view of close coupling and non -linear relationships between variables, the intelligent auto-adapted PI decoupling control method is used. From the simulation results it is found that, by bringing quadratic performance index in the single neuron, constructing adaptive PI controller, and adjusting gas flow rates through the second pressure relief valve and air compressor coordinately, both anode and cathode pressures can be maintained at ideal levels.