To understand the influences of emulsified fuel on ship exhaust emissions more comprehensively, the emissions of particulate matter (PM), nitrated, oxygenated and parent polycyclic aromatic hydrocarbons (PAHs) were studied on a ship main engine burning emulsified heavy fuel oil (EHFO) and heavy fuel oil (HFO) as a reference. The results demonstrate that EHFO (emulsified heavy fuel oil) exhibits notable abilities to significantly reduce emissions of particulate matter (PM) and low molecular weight PAHs (polycyclic aromatic hydrocarbons) in the gas phase, particularly showcasing maximum reductions of 13.99% and 40.5%, respectively. Nevertheless, burning EHFO could increase the emission of high molecular weight PAHs in fine particles and pose a consequent higher carcinogenic risk for individual particles. The total average (gaseous plus particulate) ΣBEQ of EHFO exhausts (41.5 μg/m3) was generally higher than that of HFO exhausts (18.7 μg/m3). Additionally, the combustion of EHFO (extra-heavy fuel oil) can significantly alter the emission quantity, composition, and particle-size distribution of PAH derivatives. These changes may be linked to molecular structures, such as zigzag configurations in C=O bonds. Our findings may favor the comprehensive environmental assessments on the onboard application of EHFO.