The invention discloses a self-adaptive fault-tolerant control method for a hypersonic aircraft, and the method specifically comprises the steps: carrying out the modeling of a hypersonic aircraft system, and considering the dynamic impact on the system from the modeling uncertainty of external interference and the like; establishing a robust adaptive observer by considering an H-infinity performance index, obtaining a design condition through Lyapunov stability analysis, and ensuring estimation error convergence in the presence of interference. An active fault-tolerant controller is constructed, so that a fault system is stable, and a certain H-infinity performance requirement is met. A semi-physical simulation platform of the hypersonic aircraft is built, and the effectiveness of the proposed fault estimation and fault-tolerant control scheme is verified on the semi-physical simulation platform. According to the invention, the precision of the observer is improved, and the external interference is better inhibited.