This paper describes a robust adaptive controller based on specified region pole assignment for flexible hypersonic vehicle. The dynamic model of air-breathing hypersonic vehicle retains features including flexible effects, non-minimum phase behavior, model uncertainties, and strong couplings between flight dynamic and engine. To track velocity and altitude commands, robust controller based on specified region pole assignment is used to make unstable modes of open-loop system stable and guarantee dynamic performance of attitude. Meanwhile adaptive controller is proposed to solve tracking problems when existing control failures or saturation. The simulation results demonstrate that the proposed controller achieves excellent dynamic performance while the engine operates normally.