The performance of hydrogen production by methanol steam reforming and high temperature proton exchange membrane fuel cells on drone lacks the comparison of experimental data, resulting in the overall performance improvement of the system is difficult to evaluate. Therefore, the energy management strategy of methanol reforming high temperature proton exchange membrane fuel cell hybrid power system and state machine is designed and optimized. The performance of this system is analyzed and compared with the flight experiment data of a proton exchange membrane fuel cell hybrid UAV. The results show that the SOC of the system can be stabilized between 70 and 80 during the long cruise phase. The test results show that the maximum hydrogen storage mass density of the hydrogen supply system is increased by 67.6%. The flight time of the system under economic cruise flight of the drone is improved by 29.1%–44.9% with different quality of fuel. Under the maximum flight speed of a certain wind speed, the system can meet the flight requirements and increase the flight time by 31.9% and 17.6% respectively under the wind speed of 1.5 m/s and 4 m/s. Its flight time has been greatly improved, and it has great potential as a drone system.