A method and system for control a self-energy storage multi-end flexible system are disclosed, the system controller is designed by backstepping method, which realizes the stabilization of DC voltageand the fast independent control of active and reactive power. At the same time, the constrained instruction filter is introduced to solve the problems of differential expansion and control saturationof backstepping control, and the compensation signal is designed to solve the error problem of the filter, Adaptive control is introduced to guarantee the robustness of the system to uncertain parameters, and the projection operator is used to optimize the adaptive uncertain parameters. The control law of the system is designed based on Lyapunov stability theory, which improves the anti-disturbance ability of the system and realizes the asymptotic stability of the whole system. At last, that simulation model is construct in the simulation software, and compared with the traditional PID control algorithm and the instruction filter back-calculation algorithm, the simulation result shows that the control method of the invention has bet robustness and dynamic response performance, and provides theoretical basis and technical support for the control algorithm of the self-energy storage multi-end flexible straight system.