In order to provide a theoretical basis for the development of aftertreatment devices, this paper investigated the exhaust particles of petroleum diesel (B0) and waste cooking oil biodiesel (B100) using EEPS, XPS and TGA. The results showed that the particle number distributions of different particle sizes showed a bimodal distribution. With the increase of transport distance, the peak value of the nuclear mode particles decreases and of accumulation mode particles increases. With the increase of transport distance, the O/C ratio of the particles decreased, but the ratios of sp3/sp2, C–OH and CO content increased, i.e., the farther the transport distance was, the higher the degree of disordered graphitization structure was, and the surface oxygen-containing functional groups increase. The oxidation characteristic temperature decreased with the increase of transport distance, and the activation energy of exhaust particles decreased by more than 10%, i.e., the farther the transport distance, the higher the oxidation activity of the particles. Compared with B0, B100 particles have less PN, more disordered graphitized structure, more C–OH and CO content, and higher oxidation activity. The transport distance had similar effects on the size distribution, graphitized structure, surface functional groups and oxidation activity of B0 and B100 particles.