An adaptive backstepping controller is exploited for a hypersonic vehicle in the presence of uncertain parameters and flexible dynamics. The control laws of velocity subsystem and altitude subsystem are proposed respectively based on dynamic inversion and backstepping design procedure. Low-pass first order filters are introduced to obtain the time derivatives of virtual control laws in altitude subsystem, thus to avoid the explosion of differentiation terms in traditional backstepping design. The uncertain parameters are updated adaptively by using a projection operator, and the possible parameter drift problem is eliminated. Simulation results show that the developed controller is robust to the model uncertain parameters and the flexible effects, and moreover, it can provide fine tracking performance of the velocity and altitude reference trajectories.