The development of novel technologies that can effectively solve the problems of energy shortage and environmental pollution is urgently required. To this end, a multistage integrated system coupled with a two-stroke marine diesel engine, waste heat recovery, absorption refrigeration, seawater desalination, and seawater desulfurization is designed and modeled in this study, which can reasonably utilise various forms of engine waste heat to meet the daily supply and stricter emission requirements of ships, as well as improve thermal efficiency. The accuracy of the simulation results is verified by comparing them with existing experimental data. The influence of parameters, such as the increment ratio of cycle fuel injection, expansion ratio, and evaporation pressure, on the performance of the integrated system are discussed on the basis of demonstrating the excellent transient response characteristics of diesel engines. In addition, the thermal efficiency, exergy efficiency, cooling capacity, and freshwater output are calculated under optimum operating conditions. Finally, the performance of desulfurization and the effect of the integrated system on Energy Efficiency Design Index (EEDI) are studied. The results indicate that the desulfurization rate of the integrated system is more than 94% and the EEDI meets the 2020 emission requirements. Therefore, the design is available and effective, and provides a feasible idea for researchers studying the problem of energy consumption and emissions associated with ships.