This paper develops a control method for an air-breathing hypersonic vehicle with variable geometry inlet (AHV-VGI). For the AHV-VGI, a movable translating cowl is used to track the shock on lip conditions to capture enough air mass flow, which can ensure a more powerful thrust. Compared with traditional air-breathing hypersonic vehicle with fixed geometry inlet (AHV-FGI), this AHV-VGI extends the velocity range, which is favorable to the acceleration and maneuvering flight. However, the VGI causes the unknown changes of the aerodynamic forces, moment and the thrust in the meanwhile. Therefore, we firstly establish a longitudinal dynamic for AHV-VGI, which includes the uncertain changes induced by VGI. A conception of the optimal elongation distance of translating cowl is introduced, and its estimated value is obtained by curve fitted approximation. And then, the control process for AHV-VGI is divided into two subsystems. For each subsystem, a sliding mode controller is designed, and interval type-2 fuzzy logic systems (FLSs) are adopted to approximate nonlinear parts including the uncertain changes induced by VGI. Furthermore, uniformly stability of the whole system is proved by Lyapunov approach. Finally, simulation results demonstrate that AHV have a better control performance under the condition of VGI compared to the FGI.