In this paper, the automatic identification method of the statistical energy method (SEA) subsystem is studied. The algorithm automatically identifies and establishes the SEA plate subsystems for the cruise ship from the existing finite element structure model of the ship, and creates the acoustic cavity subsystems according to the automatic search method of the established SEA plate subsystems. On the basis of which the development of the automatic SEA modeling software for the large-scale cruise ship is completed. The verification of the automatic SEA subsystem identification algorithm was completed using the cruise ship segment model, and the accuracy rate was 100% for the plate subsystems and 95% for the cavity subsystems. The proposed method improves the modeling efficiency and accuracy of the cruise SEA model, which can meet the needs and improve the efficiency of the noise analysis for the cruise ship cabins.