This paper considers robust altitude and velocity tracking of the air-breathing hypersonic flight vehicles (AHFVs). Since the non-standard dynamic characteristics of AHFVs with the aerodynamic effects make the control design challenging, we linearize the nonlinear longitude dynamics of AHFVs by the trim condition. In view of atmospheric disturbance, the control problem is described as the output tracking of multi-input-and-multi-output perturbed linear system with physical constraints of the internal states. Then the system basis transformation technique is employed to transform the plant into the dynamics with a regular form, and replace the output-tracking problem by an equivalent state tracking one. Based on the block control principle, a robust sliding surface is designed through H∞ and D-stability analysis, which provides the sliding dynamics with the suitable convergence rate and disturbance attenuation as well. Second-order sliding mode control, by means of super-twisting algorithm, is utilized to guarantee the accurate tracking and to avoid possible chattering phenomena as well. Finally, simulation results verify the effectiveness of the proposed controller.