This paper deals with fault-tolerant output tracking control for the flexible air-breathing hypersonic vehicle (AHV) subject to parametric uncertainties, external disturbances, and actuator constraints. By regarding the flexible dynamics as equivalent disturbances, the vehicle model can be split into three functional subsystems, namely, horizontal translation subsystem, vertical translation subsystem, and rotation subsystem. Then, for each subsystem, a disturbance observer is utilized to estimate the lumped effect of model uncertainties, external disturbances, and actuator faults, while a novel auxiliary system combined with the command prefilter is constructed to handle the physical constraints on actuators. Furthermore, sliding mode control is employed to design control commands for the three subsystems, sequentially. The proposed controller modifies the reference trajectories dynamically when one or more actuators become constrained, and can steer the AHV to the desired trim finally. Simulation results are provided to demonstrate the effectiveness of the designed controller.