In the field of aviation and navigation, the spline joint-flexible coupling-rotor system has been widely used. However, the installation of the spline joint and the drive shaft is easy to introduce misalignment, then affecting the safe operation of the system. To solve this problem, this paper studies the dynamic modeling and analysis of the system with misalignment. The finite element dynamic model of the system is established. In this paper, the shaft misalignment is equivalent to the spline static misalignment and the misalignment excitation force of the flexible coupling. And a general model of the spline joint is established, which introduces the static misalignment caused by the installation of the spline joint and the drive shaft, the dynamic misalignment caused by the spline joint vibration, and the tooth surface friction. By solving the dynamic equation, the effect of the misalignment on the system's dynamic characteristics is analyzed, and some suggestions and methods for health monitoring of the system are given. The accuracy of the analysis method proposed in this paper is verified by experiment. The dynamic model and the method proposed in this paper have important theoretical significance for the dynamic design and analysis of rotor systems.