The variable geometry inlet air-breathing hypersonic vehicle(VGIAHV) with movable translating cowl refers to a vehicle that has a lip in the forefront of scramjet inlet, and it is helpful to achieve the maximum capture of air stream and dramatically improve the aerodynamic performance. Considering the characters of high nonlinearity and parameter uncertainties of VGIAHV, an adaptive fuzzy control strategy based on nonlinear disturbance observer (NDO) is proposed in this paper. Firstly, the dynamic model of the VGIAHV is decomposed as a velocity subsystem and an altitude subsystem based on the backstepping method, and it is transformed into a strict form model. Then, the fuzzy logic system (FLS) combined with the adaptive technique is introduced to approximate the uncertainty terms online. Furthermore, the nonlinear disturbance observer is employed to estimate and compensate the approximation errors of the fuzzy system and modeling errors of the vehicle. Simulation results demonstrate the effectiveness of this designed controller in tracking velocity and altitude commands of the vehicle accurately and stably, and show the advantages of the variable geometry inlet for the VGIAHV.