The widespread application and increasingly stringent emission regulations call for more attention to optimize combustion process and emissions of marine diesel engine. This study conducts a numerical study to investigate the individual effect and their interaction of three post injection duration (3°CA, 5°CA and 7°CA), four spray included angles (145°, 150°, 155° and 160°) and four swirl ratios (0.5, 0.85, 1.2 and 1.6) in a marine diesel engine with main-post injection. These three parameters all exert impact on in-cylinder combustion performance and emissions by affecting fuel-air mixing quality. Results show that decreasing post injection duration from 7°CA to 3°CA shortens the combustion duration and decreases soot emission by 13.2%, while that induces a slight increase in NOx emissions by 1.0%. Spray included angle changes the spray targeting position within the combustion chamber. Wider spray included angle raises the peak value of in-cylinder pressure by 1%, decreases indicated specific fuel consumption (ISFC) by 2.9%, and produces a significantly drop in soot emission by 49.6%. The intermediate spray included angle of 150° is the most suitable in reduction of NOx emissions. Swirl ratio represents the intensity of air flow movement around the axis of cylinder. Larger swirl ratio decreases ignition delay while increases combustion duration. An appreciated swirl ratio of 0.5 achieves simultaneously reduction in NOx emissions and soot emission. To sum up, there are 13 cases that break the traditional NOx-soot trade-off relationship as both NOx and soot emissions decrease with optimized post injection duration, spray included angle and swirl ratio, in comparison with the original engine. Furthermore, an optimization procedure of case D3-A160-S0.5 is summarized, which produces the best performance in emissions and ISFC by simultaneously decreasing NOx emissions by 30.4%, soot emission by 34.6%, and ISFC by 0.7%.