Ammonia is a zero-carbon fuel with environmental and sustainable advantages, but its combustion performance is relatively poor. The poor combustion of pure ammonia can be effectively compensated by diesel ignition of ammonia. This paper investigated the impact of different diesel injection timings (ITs) on engine combustion and emission characteristics at different ammonia energy ratios. Subsequently, a response surface model was developed to optimize three parameters, namely ammonia energy ratio, injection timing, and intake pressure. The aim was to achieve an optimal trade-off between multiple objectives such as nitric oxide (NO), nitrous oxide (N2O), and unburned ammonia emissions. Advancing the injection timing has been shown to markedly improve combustion characteristics and decrease emissions of unburned ammonia. This is due to the fact that advancing the injection time provides better premixing of the ammonia-diesel fuel, which results in a more uniform and fuller combustion. It was also found that a proper reduction in intake pressure helped to reduce NO and N2O emissions. In addition, the developed response surface model was proved to be statistically significant through analysis of variance (ANOVA) test. The optimized best match is a 20.32 % ammonia energy ratio with injection timing of −18 °CA and intake pressure of 183000.13 Pa. At this time, the NO emission is 268.322 ppm, the unburned ammonia emission is 1647.947 ppm, and the N2O emission is 251.68 ppm. These findings provide a valuable reference for the research and application of ammonia-diesel dual-fuel engines.