Methanol and natural gas, as green fuels for environmental protection, have shown great potential in the field of maritime transportation. This study explores how the methanol energy fraction (MEF), exhaust gas recirculation (EGR), excess air ratio (λ), and engine injection timing (EIT) influence combustion and emission traits in marine dual-fuel (DF) engine. Initially, a DF engine model was formulated through experiments using CONVERGE software, while the CHEMKIN program devised a chemical mechanism involving 100 compounds and 512 reactions. The response surface methodology (RSM) was subsequently utilized to design the experiment and develop the regression model. The improved multi-objective particle swarm optimization (MOPSO) algorithm was applied to optimize three critical variables: brake thermal efficiency (BTE), carbon monoxide (CO), and nitrogen oxide (NOx) emissions. Ultimately, feature-optimized scenarios from the Pareto front were chosen for comparative evaluation to derive the optimal configuration. The results show that when the decision variables MEF, EGR, λ and EIT are 22.33 %, 10 %, 1.81 and 11°CA BTDC respectively, there is a better trade-off between the three target variables. Compared with the original case, the change of ITE, NOx and CO emissions in the optimal case are +0.97 %, −39.53 % and −14.51 %, respectively. Overall, based on the intelligent optimization approach, the rational selection of DF engine parameters improved the ITE and most NOx and CO emissions were effectively suppressed.