Waste heat recovery using Organic Rankine Cycle (ORC) systems shows significant potential for reducing CO₂ emissions from ships. This study designs and analyzes ORC systems for recovering multi-grade waste heat from the exhaust gas, jacket water, and scavenging air of a marine two-stroke diesel engine. A thermodynamic model is developed to investigate the effects of working fluid preheating temperature, evaporation pressure, and heat source conditions on system performance. Results show that appropriately increasing the preheating temperature of the working fluid can enhance power output. For hydrocarbons with higher critical temperatures, power output exhibits an extremum as preheating temperature increases, while for fluids with lower critical temperatures, power output increases continuously until the evaporation pressure limit is reached. Increasing evaporation pressure decreases power output but improves thermal efficiency, with a corresponding increase in heat transfer and exergy loss rates in the exhaust gas preheater. Additionally, the temperature of the heat source has an important effect on the energy and exergy balance distribution and power output of the ORC. For every 10 K rise in exhaust temperature, the bottoming cycle power output of cyclohexane increases by approximately 12.3%. This study provides theoretical support for efficient marine waste heat recovery and working fluid selection.