Hypersonic vehicle often uses a propulsion-airframe integrated design, and often has a slender body layout using thin-walled structure and lightweight materials. These factors cause serious coupling effects between propulsion system, aerodynamic force and structural deformation, then lead the ensuing special propulsion-aeroelastic coupling problems. Given these, integrated dynamic modeling and analysis methods were studied. Firstly, dynamic equations were established based on small-perturbation theory of flight dynamics. Then the sub-discipline models with both high accuracy and efficiency were employed, which were aerodynamic model based on local piston theory, structural deformation model based on modal method and quasi-one-dimensional scramjet model. Finally, a dynamic model of air-breathing hypersonic vehicle considering the coupling of propulsion system and structural deformation was established. The dynamic stability analysis of a X-43-liked two-dimensional model is carried out based on the dynamic model. The effects of propulsion and aeroelastic coupling on the dynamic characteristics of the aircraft model are analyzed, and variable parameter analysis of key coupling parameters are conducted. The results validated the feasibility of these dynamic modeling & analysis methods, and demonstrate the special influence of propulsion-aeroelastic coupling on the dynamic characteristics of the example aircraft model. The propulsion coupling can significantly reduce the Phugoid mode stability, the aeroelastic coupling can slightly increase the short period mode stability, and the elevator deflect vibration coupling can significantly reduce the short period mode stability.