This paper proposes a robust nonlinear control strategy based on adaptive backstepping method to cope with flight control for an air-breathing hypersonic vehicle with input saturation, parameter uncertainties and flexible effects.For the hypersonic-vehicle longitudinal control problem, the controller is designed separately for the velocity and height subsystems.An adaptation law derived from Lyapunov stability principle is adopted for the design of velocity subsystem controller to deal with engine physical limits, the stability of input saturation system is guaranteed.To improve robustness, a backstepping method with adaptive parameter online estimation is introduced to realize the stable tracking of altitude reference trajectory.By choosing a desirable inter-connect gain, the canard works in conjunction with the elevator to suppress the first-order mode under the excitation of control input and improve non-minimum phase behaviour.The derivatives of virtual control are achieved via a tracking differentiator.Based on the LaSalle-Yoshizawa theorem, the proposed control design is proved to be stable.Simulation results show the effectiveness of the control strategy despite the presence of parameter uncertainty, input saturation and aeroelastic effects.