In this paper, the problem of the back-stepping fault-tolerant control (FTC) based on fixed-time observer is addressed for the morphing aircraft with model uncertainties, external disturbances, and actuator faults. First, the longitudinal dynamics for the morphing process are presented, and the control-oriented models subject to undesired malfunctions are established. Second, the fixed-time observer is designed for offering estimations of compound disturbances, including system uncertainties, disturbance, and malfunction information. Especially, the observer errors could converge to zero by the proposed observer within a settling time, which is independent of the system's initial conditions. Then, a back-stepping FTC strategy based on the observations is proposed for the altitude and velocity subsystem, and the stability of the close loop system would be guaranteed by the proposed controller despite the actuator failures. Furthermore, to eliminate the effects of the "explosion of complexity" of the backstepping method, a modified dynamic surface is applied to compute derivatives of virtual laws. Finally, the numerical simulations verify the effectiveness of the proposed control approach.