Abstract: To further optimize the performance of the ammonia/diesel dual-direct-injection engine and fully exploit the great application potential of ammonia as a zero-carbon fuel in dual-fuel mode, a four-stroke ammonia/diesel dual-direct-injection engine model was established using CONVERGE software. A systematic investigation was conducted on the effects of two key variables—ammonia energy fraction (0~40%) and diesel injection timing (−9°CA~−1°CA, after top dead center) on the engine’s combustion and emission characteristics. The results indicate that an ammonia energy fraction of 20%~30% yielded the best overall performance, characterized by the shortest combustion duration, the peak cylinder pressure and average temperature, as well as the lowest unburned ammonia and greenhouse gas emissions; variations in diesel injection timing altered the in-cylinder combustion mode of ammonia/diesel mixtures, thereby influencing the trends of peak cylinder pressure, average temperature, and heat release rate; and a diesel injection timing of −7°CA, after top dead center, minimized unburned ammonia emissions and overall emission performance was optimal.