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Considered influence of nonlinear system and disturbance, a new adaptive fault-tolerant control method based on neural network model-following adaptive inversion control is introduced for flight control system in the presence of control surface damage. To restrain modeling uncertainties caused by fault system, neural network PID and inversion controllers are design for fault-tolerant flight control system. It is based on BP (back-propagation) neural network which is designed by applying improved algorithm of on-line training and parameter optimization. Moreover the output of fault aircraft can perfectly track the trajectory of the reference model. The scheme is demonstrated through simulations applying the flight control system of a fighter. The simulation results show fault-tolerant flight control system maintains stability and handling qualities.