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In order to understand the automotive PEM fuel cell system, mathematical system modeling is conducted and the model is implemented and simulated by using the Matlab®/Simulink®. The components such as fuel cell stack, air supplier, and radiator are modeled individually and integrated into a system level. The PEM fuel cell system operation control includes thermal management, air supply control, hydrogen supply control, fuel cell stack protection control, and load following control. In the thermal management, the inlet and outlet temperature of coolant are controlled to operate the fuel cell stack in desired temperature range and to prevent flooding inside the fuel cell stack. In air supply control and hydrogen supply control, the flow rates of air and hydrogen are controlled not to starve the fuel cell stack according to the output current. A control structure for the system is developed and confirmed by using the developed simulation model.