A thermal management system of a proton exchange membrane fuel cell is taken charge of controlling the temperature of fuel cell stack by rejection of electrochemically reacted heat. Two major components of thermal management system are heat exchanger and pump which determines required amount of heat. Since the performance and durability of PEMFC system is sensitive to the operating temperature and temperature distribution inside the stack, it is necessary to control the thermal management system properly under guidance of operating strategy. The control study of the thermal management system is able to be boosted up with hardware in the loop simulation which directly connects the plant simulation with real hardware components. In this study, the plant simulation of fuel cell stack has been developed and the simulation model is connected with virtual data acquisition system. And HIL simulator has been developed to control the coolant supply system for the study of PEMFC thermal management system. The virtual data acquisition system and the HIL simulator are developed under LabVIEWTM Platform and the Simulation interface toolkit integrates the fuel cell plant simulator with the virtual DAQ display and HIL simulator.