In view of the complicacy of bolted joint in diaphragm assembly of marine diaphragm coupling, the finite element model of diaphragm assembly is simplified based on the thin-layer element method, and a new simplified modeling method, structural segmentation method, is proposed. The static stiffness of the model is calculated, and the elastic modulus and Poisson's ratio of faying face element in structural segmentation method are determined. Compared with the traditional thin-layer element method, the method is of higher calculation efficiency. The modal simulation results of structure segmentation model are compared with the experimental results. The comparison results show that the vibration modes obtained by the modal analysis with structural segmentation method are in good agreement with the first three order vibration modes measured by the test, the natural frequency errors are all within 10%, and the accuracy of simplified model simulation is verified, which can provide ideas for the rapid and effective dynamic modeling of marine diaphragm assembly joint.