The design of a robust back-stepping tracking control for a flexible air-breathing hypersonic vehicle with actuator constraints is discussed. A novel auxiliary system is developed to compensate both the tracking errors and desired control laws, which guarantee the boundedness of velocity and altitude tracking errors with the physical limitations on the actuators. The sliding mode differentiator is introduced to obtain the derivatives of virtual control laws, which avoids the explosion of the differentiation term in the traditional back-stepping control algorithm. The novel nonlinear disturbance observers based on modified arctangent-based tracking differentiator(MATD) are introduced to estimate and compensate the uncertainties of the model. Finally, simulation results show the effectiveness of the proposed controller.