The effect of gear contact state change due to shaft misalignment on meshing stiffness is usually neglected in the traditional stiffness calculation model with misalignment error, the further influence mechanism of shaft misalignment on gear dynamic characteristics is also unclear. To address these shortcomings, a new mesh stiffness calculation model with misaligned gear considering the effects of tooth contact state is proposed by combining the improved loaded tooth contact analysis (LTCA) model. Then the effects of tooth contact state changes aroused by shaft misalignment on the meshing stiffness excitation are investigated. Moreover, a dynamic model of the misaligned gear system with 8 degrees of freedom (DOF) is established, and based on which the dynamic characteristics of the gear system are investigated and verified by experiment. The study results indicate that the proposed model can be used to evaluate the stiffness excitation and dynamic characteristics of the misaligned gear system with the tooth contact state taken into consideration. This study can provide a theoretical method for evaluating and identifying shaft misalignment errors.