For the purpose of revealing fully energy losses which influence the thermodynamic perfection of ship main propulsion plant integrated energy system, and acquiring energy saving measures in the daily maintenance and management of marine equipments, the mathematical models of energy and exergy balance for the system are established by using a thermodynamic exergy analysis method, and a ship sailing under stable condition is analyzed as an example. Results obtained in this paper show that the thermal efficiency of the system will be improved by adopting a waste heat recovery system, the management of the main engine is a critical factor toward ship energy saving, and exergy balance method is more reasonable than energy balance method in thermodynamic analysis. The discussions and results of the paper may provide guidance for research of the integrated energy system and the daily maintenance and management onboard a vessel.