To solve the control problem of a general hypersonic vehicle which is a strict-feedback nonlinear uncertain MIMO system, a robust backstepping control strategy based on the disturbance observer is proposed. The super-twisting algorithm is used to estimate and compensate for disturbances. The finite time convergence is guaranteed. A nonlinear backstepping control law is designed. Robust items are designed to make the whole control system has the ??2 gain which is less than or equal to the prescribed positive const. Theoretical analysis is done to validate that the system can satisfy dissipative inequality and is uniformly ultimately bounded. The simulation results show that the developed method is effective and deals with the problem of uncertain factors preferably.