This paper studies the tracking control problem of hypersonic vehicle in the process of external disturbance, parameters uncertainties and actuator faults. Firstly, a non-triangular velocity and altitude nonlinear subsystem with mismatched disturbances and actuator faults are established based on the feedback linearization model. Secondly, adaptive dynamic surface fault-tolerant controllers are designed for velocity and altitude subsystems by combining nonlinear filter, adaptive control and back-stepping method. Finally, the Lyapunov stability theory and numercial simulation are carried out to verify the availability of the proposed control strategy.