Ammonia, as a zero-carbon fuel, has the potential to serve as a medium for the production, transportation, and utilization of clean energy. The scaling up of green ammonia production also necessitates broader utilization channels for ammonia. Applying ammonia as a fuel in engines is an effective way to reduce carbon emissions. This paper employs dual direct injection technology of ammonia and diesel in a novel ammonia-fueled engine to implement various control strategies and investigates their effects on combustion and emission performance. The results indicate that when the ammonia injection timing is advanced from −40°CA ATDC to −60°CA ATDC, the flash boiling of liquid ammonia decreases the indicated thermal efficiency (ITE) below 39% and increases unburned gas emissions. Globally, injecting ammonia during the intake stroke could receive better performance. Split injection strategies of diesel significantly improve the ITE, especially under a higher pilot-injection ratio of 75%. Additionally, increasing the load benefits the ammonia combustion process. Raising the IMEP to 12 bar improves ammonia combustion efficiency to over 95%, with an ITE reaching 49%.