With the rapid growth of the cruise industry, planning ship multi-energy systems (SMES), which integrate cooling, heating, and power, has become one of the key challenges for achieving green development. To address this issue, a coordinated SMES planning method that considers carbon emissions is proposed. First, a SMES system model is constructed with a hybrid AC/DC ship power system as the core and energy conversion devices as the hubs, enabling a detailed representation of the relationship between the ship’s propulsion system and its navigation conditions. Second, considering the operational cost models of various marine equipment and relevant constraints, a bi-level optimization model for SMES planning is developed, incorporating carbon emissions. The upper level aims to minimize the total cost, while the lower level seeks to minimize both the total operational and maintenance costs and carbon emissions. Finally, the proposed model is solved using CPLEX. Simulation results validate the rationality and superiority of the proposed method.