This paper proposes a novel integrated guidance and control (IGC) method for hypersonic vehicle in terminal phase. Firstly, the system model is developed with a second order actuator dynamics. Then the back-stepping controller is designed hierarchically with command filters, where the first order command filters are implemented to construct the virtual control input with ideal states predicted by an adaptive estimator, and the nonlinear command filter is designed to produce magnitude, rate and bandwidth limited control surface deflection finally tracked by a terminal sliding mode controller with finite convergence time. Through a series of 6-DOF numerical simulations, it’s indicated that the proposed method successfully cancels out the large aerodynamics coefficient uncertainties and disturbances in hypersonic flight under limited control surface deflection. The contribution of this paper lies in the application and determination of nonlinear integrated design of guidance and control system for hypersonic vehicle.