Coating rubber claddings onto the wet surface of a ship is a widely used and very effective way on improving its UNDEX resistance. How to design good claddings has become a great concern of the Navy. In this paper, on the background of ship’s protection and conception of functionally graded materials, the in-plane dynamic crush behavior and mechanical performance of four periodic layered honeycomb claddings have been investigated at the lateral constant load. First, three groups of rubber test data are fitted with the models in ABAQUS. Then, a proper model is chosen. Moreover, the influence of compressive velocity and cell size and arrangement is analyzed from four aspects (deformation characteristic, peak reaction force, peak time and energy absorption). The results play an instructive role in understanding the dynamic behavior of claddings and provide a guideline to the selection of protective claddings and further multi-objective optimal design when subjected to UNDEX.