A dynamic system model of a proton exchange membrane fuel cell(PEMFC) has been developed. The PEMFC of this study has large active area with water cooling in order to simulate the performance of the commercially viable PEMFC system for the transportation. A PEMFC stack model is a transient thermal model which is respond to the dynamic change of the coolant temperature and the flow rate. The dynamic cooling system model has been developed to determine the coolant flow rate and the coolant temperature. Prior to the system level study, thermal management criteria have been set up and brought to the control command of the cooling system. Since the system model is designed to evaluate the effect of thermal management on the system performance, it is attempted to determine the proper control algorithm of the cooling system so that the PEMFC system is working on the thermal management criteria. As a result of simulation, feedback controlled cooling system consumes less power and produce more power comparing with that of conventionally controlled cooling system.