Taken the semi-submerged ship under ship-stacked transport mode as the research object, a three-dimensional model is built with CATIA software. Based on AQWA software, the Response Amplitude Operator (RAO) under different sea directions, speeds, and drafts in regular waves is calculated, the acceleration changes of key points of cargo lashing design under different sea conditions in irregular waves are analyzed, and the law of the influence of wave direction, speed, and draft on RAO is found. The research results can provide the motion prediction for the safe transport of semi-submerged ship under ship-stacked transport mode, and provide the basis for cargo lashing design.