A theoretical framework of nonlinear flight control for a flexible air-breathing hypersonic vehicle(FAHV) is proposed in this paper. In order to suppress the system uncertainty and external disturbance, an uncertainty and disturbance estimator(UDE) based back-stepping control strategy is designed for a dynamic state-feedback controller to provide stable velocity and altitude tracking. Firstly, the longitudinal dynamics of FAHV is simplified into a closure loop form with lumped uncertainty and disturbance. Then the UDE is applied to estimate the lumped uncertainty and disturbance for the purpose of control input compensation. While a nonlinear tracking differentiator is introduced to solve the problem of "explosion of term" in the back-stepping control. The stability of the UDE-based control strategy is proved by using Lyapunov stability theorem. Finally,simulation results are presented to demonstrate the capacity of the proposed control strategy.