In order to solve the attitude control problem of flexible hypersonic vehicles with consideration of aeroservoelastic effect, uncertainty and external disturbance, a novel moving-horizon-estimator-integrated adaptive hierarchical sliding mode control scheme is presented in this paper. First, the measurement model considering flexibility is established and the influence of aeroservoelastic effect on system stability is analyzed. Then moving horizon estimator is developed to reconstruct full state information from sensor measurements, while sliding mode disturbance observer and gain adaptation law is proposed to enhance the robustness and attenuate the chattering. Via combining moving horizon estimator, sliding mode disturbance observer, gain adaptation law and baseline hierarchical sliding mode controller, the moving-horizon-estimator-integrated adaptive hierarchical sliding mode control scheme that is able to achieve the control objective of both precise attitude control and active flexible vibration suppression is developed. Finally, Lyapunov theory is used to prove the stability of the proposed control scheme, and the numerical simulations are carried out, which further verify the effectiveness of the proposed control scheme against aeroservoelastic effect, uncertainty and external disturbance.