To improve the average efficiency of hydrogen in fuel cell vehicles, an improved thermostat control strategy based on the aging state of fuel cell is proposed. Firstly, The polarization curves of fuel cell at different aging stages were fitted by least square method. Secondly, aiming at improving the average efficiency of hydrogen, the regular parameters of thermostat control strategy were optimized continuously by using genetic algorithm. Finally, the output power of the fuel cell was determined by the improved thermostat control strategy according to the battery SOC and the regular parameters, and the 800 hours of collected data of the fuel cell vehicle was used for simulation. The results show that the improved thermostat control strategy can maintain the average efficiency of hydrogen at different fuel cell aging stages at a higher level under different cycle conditions. Compared with the common thermostat control strategy, the average efficiency of hydrogen can be increased by 1.1% at most. According to the aging state and cycle condition of fuel cell, adjusting the regular parameters of thermostat in time is beneficial to improve the average efficiency of hydrogen in the vehicle.