In order to improve the crashworthiness of the side structure of a ship’s engine room, a new crashworthiness structure of double-layer side plates is proposed in this paper. The nonlinear explicit finite element software LS-DYNA is used to simulate the collision of two ships under different schemes, and the stress situation, energy absorption and deformation of the new double-layer side plate structure are discussed and analyzed. The calculation results show that when the striking ship strikes the double-layer side plates at a speed of 5 m/s and at different impact angles of 45°, 60° and 90°, no rupture occurred in the inner plates of the double-layer side plates. The double-layered side plate crashworthiness structure can effectively prevent seawater from flooding into the engine room after a ship collision, and provide a reference for improving the side crashworthiness of the engine room during ship design and construction.