The control problem of a flexible hypersonic vehicle is presented, where input saturation and aerodynamic uncertainty are considered. A control-oriented model including aerodynamic uncertainty is derived for simple controller design due to the nonlinearity and complexity of hypersonic vehicle model. Then it is separated into velocity subsystem and altitude subsystem. On the basis of the integration of robust adaptive control and backstepping technique, respective controller is designed for each subsystem, where an auxiliary signal provided by an additional dynamic system is used to compensate for the control saturation effect. Then to deal with the βexplosion of termsβ problem inherent in backstepping control, a novel first-order filter is proposed. Simulation results are included to demonstrate the effectiveness of the adaptive backstepping control scheme