A novel nonlinear multi-input/multi-output adaptive continuous finite-time control system for air-breathing hypersonic vehicles with parametric uncertainty is proposed in this paper. The control system is based on the frame of backstepping design and time-scale separation principle to decouple the high-order vehicle model into two first-order and one second-order subsystems. For the first-order subsystems, controllers combining fast terminal sliding mode control (TSMC) with adaptive immersion and invariance (I&I) are designed. For the second-order subsystem, the controller is a combination of non-singular TSMC and adaptive I&I. The finite-time stability of each subsystem is analyzed by Lyapunov theory. Simulation experiments are conducted to demonstrate that the control system has the feature of fast and accurate tracking to attitude and velocity commands.