It is of great concern to ship designers to choose schemes with excellent comprehensive performance among many feasible ship types. The existing decision-making methods are generally highly subjective, and they need to be improved in algorithms and other aspects. In addition for different ship types the evaluation factors vary greatly. The optimization of sea-river-through container ship scheme is mainly studied here. Firstly, the main influencing factors of the preferred scheme are discussed. Secondly, the ideal solution neural network optimization model is established. Finally the feasibility and effectiveness of the model application are verified through the example analysis of 250TEU sea-riverthrough container ship. The research results can provide a reference for the design of sea-river-through container ships and similar vessels.