In view of the necessity to develop high thermal efficiency and zero-carbon engine for marine applications, this study proposes an ammonia/diesel stratified injection A-D-A(ammoniadiesel-ammonia) mode and investigates its combustion process through numerical simulations. The research findings demonstrate that the A-D-A mode is an effective approach to enhance indicated thermal efficiency (ITE), with a minimum allowable energy fraction of around 3% for the pilot diesel injection. By appropriately matching the energy fraction of the pre-injection ammonia injection and the injection interval between the pre-injection and main injection, the ITE can be maintained at a higher level while minimizing the emissions of NO_x, NH₃, and greenhouse gases (GHG) as much as possible. With a 30% energy fraction for the pre-injection ammonia, coupled with a −4°CA ATDC injection timing for the diesel injection and a 5°CA injection interval between the pre-injection and main injection, high ITE can be achieved while significantly reducing NH₃ and N₂O emissions. However, the NO_x emissions are higher compared to the original diesel engine configuration.