Regulated gaseous and particulate matter (PM) emissions in the exhaust from a heavy duty diesel engine with biodiesel fuel were studied, and the emission characteristics of PM and polycyclic aromatic hydrocarbons (PAHs) emissions in PM were highlighted. In the experiment, pure diesel fuel and B10 (a blend of diesel and biodiesel fuels with the volume ratio of 9 to 1) fuel were chosen. The study shows that, compared to the pure diesel, the emissions of PM, soluble organic fractions (SOF) and PAHs from the heavy duty diesel engine decrease when the engine burns B10 fuel, and the nitrogen oxides (NOx) emission slightly increases, while the unburned hydrocarbon (HC) and carbon monoxide (CO) emissions also decline. Among the detected 12 kinds of PAHs, emission concentrations of 10 kinds of PAHs from the engine with B10 descend. Especially Benzo(a)pyrene equivalent toxicity (BEQ) analysis results show that the BEQ of B10 fuel decreases by 15.2% compared to pure diesel. The toxicity of PAHs in exhaust particles declines when diesel engines burning biodiesel fuel.