For the problem of trajectory tracking control of a civil aircraft with pilot mishandlings and wind disturbances, a neural network based incremental nonlinear dynamic inversion (NN-INDI) controller is proposed. Firstly, a pilot model and a nonlinear dynamics model of a civil aircraft with wind disturbances are established. Secondly, the single hidden layer NN based INDI controller is designed for fault tolerant trajectory tracking control. Comparing with the conventional dynamic inversion controller, the NN-INDI controller has better adaptive capability and robustness for pilot mishandling. In addition, to solve large pilot mishandlings and strong wind disturbances, a pilot error observer and a wind observer are designed. Finally, two scenario simulations of the pilot mishandlings and unknown bounded winds show that the proposed NN-INDI controller is feasible for robust fault tolerant trajectory tracking control even in pilot mis-operations and in the wind environment.