The marine multi-gearbox system has the characteristics of multi-source excitation and multi-gearbox coupled. The interaction among gearboxes is inevitable. To reveal the coupled mechanism, a coupled dynamic model of multi-gearbox system is proposed in this paper by the generalized finite element method and the substructure method. The dynamic model of each gearbox in the multi-gearbox system is also established. Under the same working conditions, the dynamic response of single gearbox and multi-gearbox system are obtained. The results show that the adjacent gear pairs of adjacent gearboxes are more affected by the coupled effect at low rotational speed. Compared with single gearbox, the RMS curve of multi-gearbox system of meshing forces generates some new resonance peaks, which are caused by the new modes excited by the mesh frequencies of adjacent gearboxes. The dynamic response of gear pairs which are greatly affected by coupled effect are more sensitive to the change of stiffness of couplings. Reducing the stiffness of the couplings can weaken the coupled effect of the system, and vice versa. The change of housing stiffness does not influence the coupled effect of the multi-gearbox system, and the new modes and resonance peaks generated by the coupled effect have not changed significantly.