For a class of three dimensional hypersonic vehicle configuration, a physics-based vehicle model with aerodynamic/propulsion coupling is presented by using the mechanism analysis. Firstly, the motion equation of hypersonic vehicle with six degrees of freedom is derived from the Newtonian approach. Secondly, the Oblique shock and Prandtl-Meyer expansion flow theory are used to estimate the aerodynamic load on the vehicle. Differential element method is applied to calculate the forces and moments of the forebody, engine and aftbody surfaces with curved cross sections. Finally, the model is linearized under certain flight conditions. The simulation results show that the model has the couplings between the aerodynamic and propulsion system. The longitudinal and lateral modes of the model are all unstable and contain non-minimum phase phenomena.