The sub-structure modal synthesis method lends itself well to complex structures, especially when analyzing the vibration characteristics of coupled ship systems, while the transfer matrix method is characterized by its fast computation speed and low matrix order. To fully leverage the advantages of both methods, this paper integrates the free-interface substructure modal synthesis method with the multi-body system transfer matrix method, proposing a finite element modal synthesis multi-body system transfer matrix method based on free-interface substructures. Using this method, dynamic modeling and analysis were conducted for a specific ship, a close agreement was observed between the results and the simulation data. The comparison demonstrates the effectiveness and accuracy of the proposed method.