Amid increasingly stringent global environmental regulations, marine engines are undergoing an essential transition from conventional fossil fuels to alternative fuels to meet escalating regulatory requirements. This study evaluates the effects of injection pressure, the timing of ammonia injection, and the pre-injection of ammonia on combustion and emissions, aiming to identify optimal operational parameters for low-speed marine engines. A three-dimensional model of a large-bore, low-speed marine engine in a high-pressure diffusion mode was developed based on computational fluid dynamics (CFD). Simulations were conducted under 25%, 50%, 75% and 100% loads with a high ammonia energy substitution rate of 95%. The results indicate that, compared to traditional pure diesel operation, adjusting the injection pressure and the ammonia injection timing, along with employing appropriate pre-injection strategies, significantly enhances in-cylinder pressure and temperature, improves thermal efficiency, and reduces specific fuel consumption. Additionally, the dual-fuel strategy using diesel and ammonia effectively reduces nitrogen oxide emissions by up to 37.5% and carbon dioxide emissions by 93.7%.