Abstract The attitude-tracking problem of hypersonic morphing vehicles (HMVs) is investigated in this research. After introducing variable-span wings, the optimal aerodynamic shape is available throughout the entire flight mission. However, the morphing wings cause significant changes in aerodynamic coefficients and mass distribution, challenging the attitude control. Therefore, a complete design procedure for the flight control system is proposed to address the issue. Firstly, the original model and the control-oriented model of HMVs are built. Secondly, in order to eliminate the influence caused by the multisource uncertainties, an adaptive fixed-time disturbance observer combined with fuzzy control theory is established. Thirdly, the fixed-time control method is developed to stabilise hypersonic morphing vehicles based on a multivariable sliding mode manifold. The control input can be obtained directly. Finally, the effectiveness of the proposed method is proved with the help of the Lyapunov theory and simulation results.