A novel backstepping control scheme based on the fixed-time observer is proposed for the attitude control of hypersonic morphing vehicles. A fixed-time observer is used to estimate the inertial matrix uncertainty and dynamic moments caused by span variation, aerodynamic coefficient uncertainty and external environmental disturbance. It ensures that the above disturbance estimation errors can converge to zero within a fixed time, and the convergence time is independent of the initial conditions of the hypersonic morphing vehicles. Furthermore, taking into account the effects of unmatched unknown nonlinear dynamics on the attitude tacking performance, a backstepping controller is designed to compensate for the above disturbances in the system. The stability of the closed-loop system is proved based on the Lyapunov function technique. Finally, the simulation results verify the effectiveness, reliability and accuracy of the proposed scheme.