The flexible coupling-rotor system cannot be accurately reflected if the flexible coupling is viewed as a shaft or directly ignored. In order to explore accurate modeling methods on the flexible coupling-rotor system, the threaded coupling is selected as the research subject. To utilize the threaded coupling′s sensitive characteristic on misalignment failure, the finite element model of misalignment failure of the threaded coupling-rotor system is established. The higher-order nonlinear characteristic of threaded coupling is represented as a portion of valid loads and a portion of the valid stiffness matrix in each time increment. Then, setting a small misalignment angle , the key parameters are obtained when the simulated axis orbit is close to the experimental axis orbit. Subsequently, the accurate modeling of threaded coupling is established, and the misalignment of the threaded coupling-rotor system is further studied.