Abstract: The disturbance observer based control was proposed for a hypersonic vehicle controller design. Hypersonic vehicles were typically characterized by a significant degree of interaction between the highly elastic airframe and the propulsion system. A nonlinear longitudinal dynamic model considering flexible effects and the coupling between the aerodynamics and propulsion systems was established. Then, the potential sources of uncertainty for this class of vehicle were discussed and three forms of uncertainty models were developed: real parameter, unstructured, and structured. The disturbance observer based control law was designed to improve the performance and robustness for nonlinear model. Finally, the simulation results show that the proposed method is feasible.