Considering the mutual couplings in aerodynamics, propulsion and flexible structure in the hypersonic vehicle, a synthetic method of modeling is given. Firstly, the aerodynamic theory is used to estimate aerodynamic forces, thrust and flexible mode of hypersonic vehicle. The control-oriented model for a flexible hypersonic vehicle is developed. Then, the effects of aerodynamic heating and mass decrease on the natural frequencies and mode shapes, and the longitudinal aerodynamic characteristics are analyzed. The simulations show that the aerodynamic heating and mass decrease of the fuselage affect the flexible modes significantly. The control-oriented model can not only reduce the complexity of the model but also retain the coupling characteristics, and can be applied to controller design.