In this article, an adaptive fault tolerant control strategy is proposed to solve the trajectory tracking problem of a generic hypersonic vehicle subjected to actuator fault, external disturbance, and input saturation. The longitudinal model of generic hypersonic vehicle is divided into velocity subsystem and altitude subsystem, in which dynamic inversion and backstepping are applied, respectively, to track the desired trajectories. For the unknown maximum disturbance upper bound, actuator fault, and input saturation constraint, adaptive laws are proposed to estimate these information online. Finally, numeric simulation is conducted in the cruise phase for generic hypersonic vehicle. Simulation results show that the controllers designed in this article can make generic hypersonic vehicle track the desired trajectories in the presence of actuator fault, external disturbance, and input saturation.