In this study, the performance of two high-temperature proton exchange membrane fuel cell (HT-PEMFC) systems has been investigated by using the method of exergy analysis under different operating conditions, one of the systems is directly fueled by hydrogen (direct hydrogen system), and another by methane (natural gas) with steam methane reforming (reformed hydrogen system). The results indicate that for both systems, a higher fuel cell operating temperature tends to increase the efficiency and power output of the system. However, higher inlet air relative humidity and operating pressure has insignificant influence on improving the quality of both systems. Fuel cell stack is the place where exergy loss is the highest, which means more efforts should be focused on improving the energy exchange efficiency and decreasing the irreversibility of fuel cell to increase the system efficiency.