Beginning with the flight control system based on generalized inverse control method, the paper provides the system architecture based on multi-effecter control allocation and decision, and analyses the uncertainties of the control system and the robustness of the flight control system when the control performance matrix is uncertain. To solve the problem of control error of the current open-loop generalized inverse control system, a generalized inverse control system based on closed-loop feedback is established, and the robust design of the flight control system is realized. The simulati on is carried out aiming at the uncertainty problem of advanced aircraft. Results show that the generalized inverse control system based on closed-loop feedback can solve the robustness of the system under the control uncertainty matrix effectively, which plays a positive role on promoting the practical application in the project.