Hypersonic morphing vehicles enhance aerodynamic performance through dynamic external configuration adjustments. By integrating morphing commands as dynamic control inputs rather than predefined ones, the vehicle achieves improved adaptability to varying flight conditions. However, this introduces significant coupling between morphing and attitude control loops. This paper proposes the Morphing-Aerodynamic Collaborative Control Algorithm (MACC), which incorporates morphing parameters into the control input vector, enabling autonomous adaptation to environmental changes.The MACC framework leverages dynamics and aerodynamic models for hypersonic vehicles with variable wingspan and sweep angle. The control layer uses a nonsingular fast terminal sliding mode controller to generate robust virtual commands. A third-order tracking differentiator with fixed-time convergence ensures precise guidance command tracking, offering rapid responses and maintaining fixed-time convergence within predefined bounds. Additionally, a fixed-time convergent extended state observer (ESO) estimates system disturbances, providing real-time compensation for unmodeled dynamics and external perturbations. The observer parameters are analytically derived to simplify tuning and reduce implementation complexity.Control allocation is optimized using a modified sequential quadratic programming algorithm. Numerical simulations validate MACC’s effectiveness in attitude control, and Monte Carlo analysis confirms its robustness under severe aerodynamic disturbances. The fixed-time convergence properties of the tracking differentiator and ESO improve transient performance, ensuring rapid disturbance attenuation even with abrupt configuration changes.