PM (particulate matter) emissions from ships are the main sources of marine atmosphere pollution. Controlling the emissions of particulate matter from ships is related to the sustainable development of the shipping industry. To reduce PM emissions from marine four-stroke diesel engines, DPFs are effective. Our results show that DPF had more than 90% capturing efficiency for both the number and mass emissions of PM, and the capturing efficiency for the accumulation mode was higher than that of the nuclear mode. DPF can also significantly reduce the chemical components of PM in marine diesel exhaust gas. The removal efficiencies for OC and EC were 89.7–91.6% and 84.8–92.8%, respectively, with each particle size range showing over 80% efficiency. SO42− was the ion with the highest content, followed by NH4+, NO3−, Na+, NO2−, and Cl−, with their reduced proportions remaining consistent with the removal efficiency of particulate matter. DPF can also effectively reduce PAH content and toxicity. The use of DPF can greatly improve the impact of ship emissions on the marine atmospheric environment. The appropriate DPF with the best performance can be selected according to the exhaust parameters and particle size distributions with different characteristics.