In order to study the safety of a large motor transport ro-ro (PCTC) ship in the typhoon environment, this paper uses Ansys-aqwa software to design and analyze the initial mooring scheme layout of the wharf twin ships based on the numerical calculation and analysis method of three-dimensional potential flow theory, explores the shortcomings of the initial mooring scheme layout, and further optimizes the adjustment and numerical simulation of the initial mooring scheme layout of the wharf twin ships. The optimization of the motion response of the two vessels after the adjustment of the mooring scheme and the safety of the cable were analyzed. The results show that under the optimized mooring scheme, the motion response and cable tension of the two ships are significantly improved, and the maximum cable tension is optimized to decrease by 26.7%, and the mooring can be normal in typhoon environment. The research results can provide a basis for the safe mooring of multiple ships side by side in similar wharves under harsh environmental conditions in the future.