This paper deals with an autonomous flight controller design problem for a tilt-rotor aircraft in rotary-wing mode. The inner-loop algorithm is designed using the output-based approximate feedback linearization. The model error originated from the feedback linearization is cancelled within allowable tolerance by using single-hidden-layer neural network. According to Lyapunov direct stability theory, the adaptive update law is derived to run the neural network on-line, which is based on the linear observer dynamics. Moreover, the outer-loop algorithm is designed to track the trajectory generated from way-point guidance. Especially, heading and flight-path angle line-of-sight guidance are applied to the outer-loop to improve accuracy of the landing tracking performance. The 6-DOF nonlinear simulation shows that the overall performance of the flight control algorithm is satisfactory even though the collective input response shows instantaneous actuator saturation for a short time due to the lack of the neural network and the saturation protection logic in that loop.