In order to investigate the mechanism on the microstructure of soot by adding biodiesel to diesel, the soot of biodiesel/diesel mixed fuel was collected by a constant volume combustion chamber, and the microstructure characteristics of soot were studied by SAXS and HRTEM techniques. The results showed that the added biodiesel reduced the delay of ignition and advanced the peak time of soot generation. The particulate matter in soot underwent a deep internal and external oxidation process. The accumulation of internal oxidation products forms a certain filling effect, which affects the subsequent oxidation rate. The microstructure of the single particulate matter was further refined to a cylindrical-like 3D sub-model filled with voids. The improved sub-model optimizes the DPF pressure drop model and provides a potential research basis for the DPF catalytic oxidation and regeneration model.