In this paper, the hypersonic aircraft model is divided into several substructures according to its structure and shape characteristics. Furthermore, the hysteresis nonlinearity of wing-fuselage connection which is caused by relaxation and friction is within consideration. The third-order piston theory and strip theory is employed to obtain the distribution of nonlinear aerodynamic force which is applied upon the wings. By means of free interface modal synthesis of dynamic substructure method, the nonlinear dynamic model of hypersonic aircraft is obtained. Then, through numerical simulation method, this paper researches on the model’s dynamic response and bifurcation characteristics, which is influenced by different hysteresis nonlinear structure parameters. In the end, it is showed that the parameter of hysteresis nonlinearity has a great impact on response and bifurcation characteristics of the system.