The proton exchange membrane fuel cell (PEMFC) stack is a key component in the fuel cell/battery hybrid vehicle. Thermal management and optimized control of the PEMFC under real driving cycle remains a challenging issue. This paper presents a new hybrid vehicle model, including simulations of diver behavior, vehicle dynamic, vehicle control unit, energy control unit, PEMFC stack, cooling system, battery, DC/DC converter, and motor. The stack model had been validated against experimental results. The aim is to model and analyze the characteristics of the 30 kW PEMFC stack regulated by its cooling system under actual driving conditions. Under actual driving cycles (0–65 kW/h), 33%–50% of the total energy becomes stack heat; the heat dissipation requirements of the PEMFC stack are high and increase at high speed and acceleration. A PID control is proposed; the cooling water flow rate is adjusted; the control succeeded in stabilizing the stack temperature at 350 K at actual driving conditions. Constant and relative lower inlet cooling water temperature (340 K) improves the regulation ability of the PID control. The hybrid vehicle model can provide a theoretical basis for the thermal management of the PEMFC stack in complex vehicle driving conditions.