In order to probe into the design of multi-layered protective structure, the finite element method was used to simulate the typical mode and the preliquid cabin mode of the same multi-layered protective structure, and the validity of numerical simulation method was verified by comparison of the typical mode and experimental results. The influences of the pre-liquid cabin mode on the dynamic response process, the failure mode and the protective efficiency of the multi-layered protective structure were analyzed specifically, and its forming mechanism was analyzed. The differences between the two modes were compared from the following three aspects: the structure failure process, the load characteristics and the energy absorption characteristics. Finally, the protective mechanism of multi-layered protective structure is discussed, which provides a reference for the engineering design of underwater broadside protection structure of surface vessels.