In this paper, a mathematical modeling was developed to simulate 1kW class air cooled Polymer Electrolyte Membrane Fuel Cell(PEMFC) system. The proposed modeling was conducted under SIMULINK based environment. The model ing was developed based on the thermodynamic and chemical equilibrium. The objective is to design and implement the entire fuel cell system model ing including the system controller modeling. The fuel cell process and the control system modeling should have to be connected with each other simultaneously， therefore the two types of modeling influences each other when the system simulator run. The fuel cell modeling libraries are simulated using the SIMULINK under the thermodynamic and chemical equilibrium base. The PID controller application was designed and developed to test the process modeling and verify it. This the prototype development of the fuel cell system to design and test more complicate fuel cell systems, like the residential power generation system. The simulation results was compared to the real PEMFC system performance. We have achieved the reasonable accordance with the Lab test and the simulation results.