An integrated flight control system was designed according to the six DOF nonlinear general model of pitching channel of hypersonic vehicle. The system has an integrated flight control loop, which is composed of one fuzzy controller and two PD controllers. Based on genetic algorithm, the optimization process of fuzzy control rules and PD feedback parameters was carried out automatically, which means experts- knowledge and training data were not necessary in advance, so the problem of obtaining fuzzy logic control rules was solved. Nonlinear dynamics, parameter uncertainties and constraints were concerned in the 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, especially obtaining superior robustness compared to conventional double loop flight control system, which is based on the same basic control strategies and optimization tool.