International Maritime Organization (IMO) proposed the Energy Efficiency Operation Indicator (EEOI) in 2005 and the Energy Efficiency Design Index (EEDI) in 2008 so as to address emission concern and regulation. Likewise, Ship Energy Efficiency Management Plan (SEEMP) and Greenhouse Gas (GHG) monitoring and management are also becoming an issue lately. This paper introduces the energy efficiency design index (operation indicator) monitoring system (EDiMS) software can continuously monitor $CO_2$, $NO_x$, $SO_x$, and PM values emitted from ship. The accurate inventory of ships GHG can be obtained from base of emission result during the engine shop test trial and the actual monitoring of shaft power and ship speed. In addition, the ability to store all exhaust emission and engine operation data can be applied as the useful tool of the inventory work of air pollution and ship energy management plan for the mitigation or reduction of ship emissions.