In this paper, an improved adaptive fault-tolerant control (FTC) scheme is presented based on an extended state observer (ESO) for a highly maneuverable variable structure fighter (VSF) with simultaneous faults of the rudder surface and sensor. The feedback linearization model of the attitude system with faults and external disturbances is introduced. In order to realize the real-time observation of the rudder and sensor faults, a neural network estimator is used to approximate sensor faults, and the ESO is designed to estimate the rudder surface fault and attitude variables. On this basis, the estimated value is used to replace the measured value for state variables to design the adaptive fault-tolerant controller for the inner and outer loop, combined with the second-order command filter to offset the phenomenon of backstepping differential amplification system noise. Finally, the proposed FTC scheme realizes the variable structure self-repairing of multiple positions, multiple types of faults in VSF using fault estimation. The Lyapunov theory and Barbalat’s lemma prove the stability of the designed observer and controller. The effectiveness of the FTC scheme is verified by a simulation experiment.