The continuous development of spacecraft with large flexible structures has resulted in an increase in the mass and aspect ratio of launch vehicles, while the wide application of lightweight materials in the aerospace field has increased the flexible modes of launch vehicles. In order to solve the problem of deviation from the nominal control or even destabilization of the system caused by uncertainties such as unknown or unmodelled dynamics, frequency perturbation of the flexible mode, changes in its own parameters, and external environmental disturbances during the flight of such large-scale flexible launch vehicles with simultaneous structural deformation, rigid-elastic coupling and multimodal vibrations, an improved adaptive augmentation control method based on model reference adaption, and spectral damping is proposed in this paper, including a basic PD controller, a reference model, and an adaptive gain adjustment based on spectral damping. The baseline PD controller was used for flight attitude control in the nominal state. In the non-nominal state, the spectral dampers in the adaptive gain adjustment law extracted and processed the high-frequency signal from the tracking error and control-command error between the reference model and the actual system to generate the adaptive gain. The adjustment gain was multiplied by the baseline controller gain to increase/decrease the overall gain of the system to improve the system’s performance and robust stability, so that the system had the ability to return to the nominal state when it was affected by various uncertainties and deviated from the nominal state, or even destabilized.