The polycyclic aromatic hydrocarbons (PAHs) were measured by glass fiber filter and XAD-2 collector, ultrasonic extraction, soxhlet extraction and GC-MS analysis equipment. The exhaust emission of the DI single cylinder diesel engine fueled with pure diesel, biodiesel and biodiesel blends of 50% (B50) were measured. The results indicate that the particle-phase PAHs emissions of diesel engine decrease with the increasing of load. The gas-phase PAHs emissions of diesel engine decrease with the increasing of load in the beginning and it turns to going up with further increasing of load. The particle-phase and gas-phase PAHs emissions of biodiesel decrease and mean concentration are lower than that of diesel. The total PAHs emission concentration of biodisesl is 41.1-70.1 microg/m3. Total PAHs mean concentration emissions of biodiesel is decreased 33.3% than that of diesel. The mass proportion of three-ring PAHs emissions of those 3 kinds tested fuels is about 44% in the total PAHs. Biodiesel can increase the proportion of three-ring PAHs. Toxic equivalence of PAHs emissions of biodiesel are greatly lower than that of diesel. It is less harmful to human than diesel fuel.