Hypersonic vehicles often use the aerodynamic configuration and light materials such as lifting body and waverider, which leads to the unmatched uncertain control problems caused by strong coupling characteristics and interference during reentry. To solve these problems, firstly, this paper analyzes the key factors and uncertainties that affect the attitude motion of hypersonic vehicle. Secondly, it studies the modeling and verification of rigid body and elastic body of hypersonic vehicle, establishes the error model with disturbance observation compensation, and proposes a new attitude control scheme of hypersonic vehicle, which realizes the stable tracking of attitude angle and improves the uncertainty of key parameters of the system. The simulation results show that the performance index meets the requirements and has good robust performance in the presence of unknown disturbance.