The sandwich plate can be used to replace the conventional steel stiffened plates on the ship’s hull structure. By using the sandwich plate, not only the stiffness of the plate can be increased but also the overall ship weight can be reduced, as well as the ship payload can be increased. The sandwich plate should be accompanied by the damage identification system to prevent ship structural failure. In this paper, the global damage identification method, which is based on the vibration analysis, is investigated. For that purpose, the vibration-based damage identification using the Finite Element Method (FEM) is explored. The variables being investigated are the damage sizes, damage locations, and the boundary conditions which affect the natural frequencies of the structures. The sandwich plate considered in this study consisted of steel faceplates with the polyurethane elastomer core, which has been checked to meet Lloyd’s register, an international maritime standard. From the analysis, it is found that the fully clamped boundary conditions accompanied by high vibration modes are more sensitive to the presence of artificial damage. The changes in the natural frequencies can be used as a reference to identify the size and location of damage in the sandwich plate.