The invention discloses an electro-hydrostatic actuation system double-closed-loop model reference adaptive control method which includes the following steps: an actuator pressure difference inner loop control system is constructed, and the damping of an electro-hydrostatic actuator is increased; a feedback channel high-pass filter is added to the actuator pressure difference inner loop control system to eliminate the reduction in stiffness of the electro-hydrostatic actuator caused by damping increase; a model reference adaptive control method is adopted to improve the adaptability to the inherent uncertainty of the actuation system; and a signal-based control output compensator is used to make compensation for the equivalent output control of an adaptive regulator to get the equivalent output of the adaptive regulator after compensation, and the response precision and sensitivity of the system under small signal task instructions are improved. Through the method, the dynamic performance of the system can be adjusted flexibly according to the actual working condition, the speed of response under large signal task instructions is increased, and the sensitivity and accuracy of the system under small signal task instructions are improved significantly.