Aiming at the problem of insufficient endurance performance of flapping wing aircraft, a stable attitude control algorithm based on energy optimization and ESO (extended state observer) is designed, which effectively reduces the energy consumption in cruise phase. Firstly, the longitudinal dynamic model of flapping wing aircraft is established, and then the uncertain part of the system and various unknown external disturbances are taken as the total disturbance. ESO module is introduced to observe and track the total disturbance in real time. Therefore, the system is transformed into a series integral system through the total disturbance feedback, and then the energy optimal control law is designed on the base of the transformed system. The numerical simulation results show that, compared with the traditional PID control method, the designed energy optimal control method reduces the average energy consumption by 35.28%.