For the problem of hypersonic flight vehicle (HFV) tracking performance with uncertain parameters and external disturbances, a backstepping control scheme based on finite time prescribed performance is proposed. Firstly, in order to facilitate the controller design, the HFV model is divided into velocity and height subsystems. Then, the controllers based on prescribed performance are designed for the these subsystems respectively to improve the transient performance and steady state performance of the system. The tracking error is guaranteed to converge to the steady state within the setting time by designing a finite-time performance function. In addition, considering the difficulty in obtaining the derivative of virtual command and the influence of disturbance items on the system in the backstepping controller design, an estimation method based on disturbance observer is proposed, which aims to simplify the controller design process and reduce its complexity while achieving great observation effect of disturbance. It is proved that the tracking errors of the system are uniformly bounded based on Lyapunov stability theory. Finally, the simulation results show the effectiveness of the proposed method.