This paper presents an adaptive neural control for the longitudinal dynamics of a morphing aircraft. Based on the functional decomposition, it is reasonable to decompose the longitudinal dynamics into velocity and altitude subsystems. As for the velocity subsystem, the adaptive control is proposed via dynamic inversion method using neural network. To deal with input constraints, the additional compensation system is employed to help engine recover from input saturation rapidly. The highlight is that high order integral chained differentiator is used to estimate the newly defined variables and an adaptive neural controller is designed for the altitude subsystem where only one neural network is employed to approximate the lumped uncertain nonlinearity. The altitude subsystem controller is considerably simpler than the ones based on backstepping. It is proved using Lyapunov stability theory that the proposed control law can ensure that all the tracking error converges to an arbitrarily small neighborhood around zero. Numerical simulation study demonstrates the effectiveness of the proposed strategy, during the morphing process, in spite of some uncertain system nonlinearity.