The stiffened plate is the main type of transverse bulkhead structure in the mainstream large ships, but the stiffened plate is limited by its single-layer structure characteristic, so it is difficult to propose a new design. A kind of corrugated sandwich plate is designed and applied to the transverse bulkhead structure in the large ships. A simplified numerical model is established using the finite element software, and the dynamic response and failure mechanism of transverse bulkhead structure in corrugated sandwich plate under high-speed fragment penetration are studied and compared with the transverse bulkhead structure in traditional single-layer stiffened plate. The results show that the anti-penetration performance of transverse bulkhead structure is improved obviously by the corrugated sandwich plate.