An adaptive backstepping controller based on nonlinear disturbance observer was designed to solve the problem of parameters uncertainty in elastomer model of hypersonic vehicles. The curve-fitted model was expressed as strict feedback form and the method of backstepping was used to design the controller. Dynamic surface method was introduced to obtain the derivatives of virtual control amount, which avoided the explosion of differentiation terms in the traditional backstepping control. In order to enhance the controller’s robustness, a new nonlinear disturbance observer which was based on second order tracking-differentiator was introduced to estimate and compensate the model uncertainties adaptively. Simulation results demonstrate that the controller has high robustness to the model uncertainties and aerodynamics and it can track the reference instructions of velocity and altitude steadily.