The ship industry is currently facing numerous challenges, including rising fuel prices, limited fuel resources, and increasingly strict regulations related to energy efficiency and pollutant emissions. In this context, the adoption of green-ship wind–photovoltaic–electricity–fuel multi-energy supply systems has emerged as an efficient and clean technology that harnesses multiple energy sources. These systems have the potential to increase the utilization of renewable energy in ship operations while optimizing management practices in order to enhance overall energy efficiency. To address these challenges, this article presents a comprehensive energy supply system for ships that integrates multi-energy sources for cold–heat–electricity supply. The primary components of this system include fuel cells, photovoltaic equipment, wind turbines, electric heating pumps, electric refrigerators, thermal refrigerators, batteries, and heat storage tanks. By ensuring the safety of the system, our approach aims to minimize daily operating costs and optimize the performance of the multi-energy flow system by running scheduling models. To achieve this, our proposed system utilizes dynamic planning techniques combined with ship navigation conditions to establish an optimized management model. This model facilitates the coordinated distribution of green ship electricity, thermal energy, and cooling loads. The results of our study demonstrate that optimized management models significantly reduce economic costs and improve the stability of energy storage equipment. Specifically, through an analysis of the economic benefits of power storage and heat storage tanks, we highlight the potential for reducing fuel consumption by 6.0%, 1.5%, 1.4%, and 2.9% through the use of electric–thermal hybrid energy storage conditions.