Shaft misalignment will change the gear contact state, and then leads to the variation of the internal stiffness excitation of the gear pair, and finally the dynamic characteristics of the gear system will be affected. However, the influence of the gear contact state change on stiffness is usually neglected in the traditional stiffness calculation model for misaligned gears, and the underlying influence mechanism of the gear contact state changes aroused by the shaft misalignment on the dynamic characteristics of gear system is still unclear. To address these shortcomings, traditional loaded tooth contact analysis (LTCA) model is improved with the influences of fillet foundation deformation taken into consideration. Combined with the improved LTCA model, a new mesh stiffness calculation model for misaligned gear considering the tooth contact state is proposed, and then the effects of the contact state changes aroused by the shaft misalignment on the mesh stiffness excitation are studied. Moreover, a dynamic model of misaligned gear system with 8 degree of freedom (DOF) is established, and the dynamic characteristics of the system are simulated and finally verified by experiment. The results show that the proposed model can be used to evaluate the dynamic characteristics of the misaligned gear system with the change of gear tooth contact state taken into consideration. This study provides a theoretical method for the evaluation and identification of the shaft misalignment error.