Overall system performance of hydrogen fuel cell system in a compact special vehicle is mostly influenced by thermal characteristics in chemical operation mechanism and heat dissipation with air flow. This study analyzes electrical output and air cooling characteristics of the fuel cell system with numerical methods. The heat generation rate were predicted with the output, and cooling characteristics around the radiator system were analyzed with air flow generated by the vehicle movement. The results showed that the fuel cell performance was largely connected with complicated air flow near the special vehicle.