Tests were conducted by using TSI EEPS3090 particle size spectrometer to study the effect of fuel with different physical and chemical properties on particle size distribution in common rail diesel engine. For the fuels of different cetane number, the particle size was mostly between 5nm and 300nm and the particle size distributions were unimodal with peaks at 30nm with medium or small load. Increasing cetane number appropriately could make the ignition delay period shorter and the sustained combustion period longer, which would drop the number of nuclei mode particles. Meanwhile，the number of nucleation mode particles increased with more sulphur in the fuel. With the cetane number increased, the percentage of SOF decreased and the percentage of DS increased.