An analysis program to simulate the operation of a polymer electrolyte membrane fuel cell (PEMFC) system was set up, and system operation with variations in the working conditions of various components (especially the thermal management system) was simulated. The entire system included a PEMFC stack and balance-of-plant components such as an air-supply unit, a fuel-supply unit, and a heat-management unit (cooling system). Thermodynamic models of all components were made to evaluate the design performance of the entire system, and then off-design models were set up to simulate the operation of the entire system under arbitrary working conditions. A parametric study was carried out to examine the effects of varying the operating conditions (especially the ambient conditions and the operating conditions of the cooling system) on the operation and performance of the entire system.