The effect of biodiesel produced from waste cooking oil (WCO) on the soot particles in a compression ignition engine was investigated and compared with conventional diesel fuel. The indicated mean effective pressure of approximately 0.65 MPa was tested under an engine speed of 1200 revolutions per minute. The fuels were injected at an injection timing of −5 crank angle degree after top dead center with injection pressures of 80 MPa. Detailed characteristics of particulate matters were analyzed in terms of transmission electron microscopy (TEM), thermogravimetric analysis (TGA) and elemental analysis. Soot aggregates were collected on TEM grid by thermophoretic sampling device installed in the exhaust pipe of the engine. High-resolution TEM images revealed that the WCO biodiesel soot was composed of smaller primary particle than diesel soot. The mean primary particle diameter was measured as 19.9 nm for WCO biodiesel and 23.7 nm for diesel, respectively. WCO biodiesel showed faster mass reduction of soot particles according to surrounding temperature by TGA analysis. While the oxidation of soot particles from diesel continued until 933K, WCO biodiesel soot oxidation terminated at 833K. From elemental analysis, it was revealed that the diesel soot was mainly composed of carbon and hydrogen. On the other hand, WCO biodiesel soot contained high amount of oxygen species.