To improve the utilization of electric energy and heat energy of the fuel cell stack, it is necessary to explore the composition and availability of stack energy under different operating conditions. In this paper, a dynamic stack model that can quantitatively calculate the energy flow and thermal voltage is established, and the actual operation data of a 90 kW stack is used as model input and parameter identifications. Besides, the energy flow and thermal voltage of the stack are simulated and compared under different operating conditions, including different cathode inlet relative humidity, stack temperature, pressure, and oxygen excess ratio. According to the analysis results, for the 90 kW fuel cell stack, the gas emissions can take away about 30 kW of waste heat under the maximum power condition, which accounts for as considerably large as 28% of the heat generated by the stack. Moreover, it is indicated that the self-humidifying stack has a relatively small thermal voltage of about 1.24 V, and the thermal voltage increases by about 0.02 V for every 10% increase in the cathode inlet humidity after the cathode humidity reaches saturation. These conclusions are of great economic significance for improving the electric energy and waste heat utilization of water-cooled PEMFC.