The integration of waste-driven absorption refrigeration technology into marine applications is recognized as a promising low-carbon solution. Nonetheless, its practical application does not inherently outperform electric compression technology, primarily due to the absorption system's inherent thermal inertia and limited adjustability. This characteristic renders the system less responsive to the dynamic refrigeration requirements typically encountered on board vessels. In this study, a shipborne ammonia absorption refrigeration–ice storage system is proposed to balance the cooling load between supply and demand. To evaluate the efficiency of the integrated system for ice storage and cooling during ship sailing, key operational variables including refrigeration temperature, cooling water temperature, and generation temperature are analyzed to assess the thermal cycle performance of the system. A typical shipping route is considered for cooling operation optimisation of the absorption refrigeration–ice storage system. This paper explores four typical cooling-supply strategies and determines the operation modes for the ice storage period and the cooling period based on considerations of energy consumption, energy utilization, and economic factors. The final optimisation results indicate that the combined system has significant advantages based on energy consumption and operation cost. In comparison to compression and absorption refrigeration systems, the proposed system exhibits 52.4% and 8.31% reductions in energy consumption, respectively. Additionally, the operation costs are decreased by 12.27% and 27.41%, respectively, and the life cycle costs are lowered by 11.51% and 32.35%, respectively. The findings of this combined system can provide a technical reference for the design and operation of a ship waste-heat refrigeration system.