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The effects of heavy fuel oil and biodiesel blends on engine combustion and emissions were studied in a marine two-stroke diesel engine. The engine was operated under propeller conditions using five different fuels with biodiesel blends of 10% (B10), 30% (B30), 50% (B50), and sulphur contents of 0.467% low sulphur fuel oil (LSFO) and 2.9% high sulphur fuel oil (HSFO). Tests have shown that using a biodiesel blend increases the engine fuel consumption due to its lower calorific value. Heavy fuel oil has a high Polycyclic aromatic hydrocarbons (PAH) content, which leads to higher exhaust temperatures due to severe afterburning in the engine. A comparison of engine soot emissions under different fuel conditions was carried out, and it was found that the oxygen content in biodiesel promoted the oxidation of soot particles during the combustion process, which reduced the soot emissions of biodiesel. Compared to HSFO, B10, B30, B50 and LSFO, the soot emission concentrations were reduced by 50.2%, 56.4%, 61% and 37.4%, respectively. In our experiments, the soot particles in the engine exhaust were sampled with a thermal float probe. Using Raman spectroscopy analysis, it was found that as the biodiesel ratio increased, the degree of carbonisation of the soot particles in the exhaust became less than that in the oxygenation process, resulting in a decrease in the degree of graphitisation.