Considering the pitching channel of air breathing hypersonic vehicle X-43A as plant, flight control system was designed according to the 6 degree of freedom nonlinear model. The flight control system includes two loops, of which the structure is conventional mode. The guidance loop is a PD controller, while the control loop is composed of two fuzzy logic controllers. The guidance loop leads the vehicle to follow trajectory, when the control loop follows guidance command. Based on genetic algorithm, the optimization process of PD feedback parameters and fuzzy logic control rules was carried out automatically, which means expert knowledge and training data are not necessary in advance. This optimization process solved the problem of obtaining fuzzy logic control rules. Nonlinear dynamics, uncertainties and restrictions were contained in research on the control of trajectory, attitude and thrust. Simulations show that the method is able to satisfy both the robustness of flight control system and the convergence of optimization process on request.