Methanol is a promising low-carbon fuel that can effectively reduce environmental pollution from ships compared to traditional fuels. The timing of methanol injection is a major factor affecting the performance of internal combustion engines, and either too late or too early injection can severely impact the combustion efficiency of an engine. This paper focused on a 4135Aca marine diesel engine produced by the Shanghai Diesel Engine Factory in China. Using CONVERGE/3.0 software for numerical simulation, the study analyzed the impact of methanol injection timing on the combustion and emission characteristics of marine diesel engines. It was found that the determination of methanol injection timing should comprehensively consider the effects of the combustion start point, mixture quality, flame front propagation speed, and evaporation heat absorption. Appropriate methanol injection timing can improve the combustion duration, cylinder pressure, and heat release rate, enhancing the power performance of marine diesel engines. This study shows that methanol injection at −30 °CA can effectively control the in-cylinder combustion process, improve combustion efficiency, and significantly reduce the emissions of pollutants such as soot (by 60.5%), HC (by 3.6%), CO (by 95.3%), etc. However, it can lead to an increase in NOx (by 3.7%) generation under high-temperature conditions. This research can provide a certain reference for the engineering application of methanol direct injection engines for ships.