Low-speed two-stroke marine diesel engines dominate the modern global long-distance transportation market; with the increasingly stringent regulations, the combustion and emissions of these engines is gaining intense interest. The primary objective of the present study was to understand the effects of air-fuel mixing by pilot injection strategy on the combustion and emission characteristics of the marine diesel engines through a numerical study. Specifically, a computational fluid dynamic (CFD) model was established and validated by experimental data for a typical low-speed two-stroke marine diesel engine. The combustion parameters under different stages were analyzed, including mean in-cylinder temperature and pressure, indicated thermal efficiency (ITE), indicated specific fuel consumption (ISFC), and distribution of fuel-air mixture. Results indicated that, due to the premixing effect, the pilot injection produced unburned soot from the main injection’s ignition as well as decrease the intervals between the middle and final stages of combustion, thus raising the in-cylinder temperature. The interaction between the reduction of soot particles resulted from the increased temperature, and the decrease of the stage intervals led to lower overall boundary heat loss, which improved the effective thermal efficiency. The pilot injection timing and quality, respectively, showed quadratic and linear impact modes on engine performance and emissions.