To improve the combustion efficiency and indicated thermal efficiency of ammonia diesel dual-fuel engines while reducing pollutant emissions, based on a large-bore marine engine, the 3D simulation software CONVERGE was used to analyze the combustion and emissions under different ammonia energy substitution ratios, different diesel injection timings and initial cylinder temperatures. The results show that with the gradual increase of ammonia energy substitution ratio and the increase of premixed combustion, the indicated thermal efficiency of the engine is improved, and the carbon emission is significantly reduced. However, the excessively high ammonia substitution ratio reduces the completion of combustion and the combustion efficiency, thereby decreasing the indicated thermal efficiency. When the diesel injection timing is appropriately advanced, the combustion efficiency is improved while the NH₃ and CO emissions are reduced. Increasing the initial temperature in the cylinder improves the combustion environment, promotes the combustion rate of ammonia fuel, improves the indicated thermal efficiency of the engine, and significantly reduces N₂O and unburned ammonia emissions. At an ammonia substitution ratio of 40%, a diesel injection timing of -21°, and an initial cylinder temperature of 338 K, the engine’s indicated thermal efficiency reached the highest level of 51.37%, while the N₂O and unburned ammonia emission levels were very low.