A two-dimensional thermal model of proton exchange membrane fuel cell with large active area is developed to investigate the performance of fuel cell with large active area over various thermal management conditions. The core sub-models of the two-dimensional thermal model are one-dimensional agglomerate structure electrochemical reaction model, one-dimensional water transport model, and a two-dimensional heat transfer model. Prior to carrying out the simulation, this study is contributed to set up the operating temperature of the fuel cell with large active area which is a maximum temperature inside the fuel cell considering durability of membrane electrolyte. The simulation results show that the operating temperature of the fuel cell and temperature distribution inside the fuel cell can affect significantly the total net power at extreme conditions. Results also show that the parasitic losses of balance of plant component should be precisely controlled to produce the maximum system power with minimum parasitic loss of thermal management system.