To reduce air pollution and the reliance on fossil fuel, biodiesel has been widely investigated as an alternative fuel for diesel engines. The purpose of this study is to investigate the influence of waste cooking oil (WCO) biodiesel on the physical properties and the oxidation reactivity of the particles emitted by a diesel engine operating on WCO biodiesel as the main fuel. Experiments were conducted on a direct-injection diesel engine fueled with biodiesel, B75 (75% biodiesel and 25% diesel on volume basis, v/v), B50, B20, and diesel fuel, at five engine loads and at an engine speed of 1920 rev/min. Particulate samples were collected to analyze the particulate nanostructure, volatility, and oxidation characteristics. Biodiesel or low-load operation leads to smaller primary particles and more disordered nanostructures having shorter and more curved graphene layers. It can be found that particles from biodiesel, blended fuels, or low-load operation have higher volatile mass fractions and faster oxidation reaction rates than particles from diesel or heavy-load operation. The higher oxidation reaction rates are due mainly to the smaller particle size, the more disordered nanostructure, and the higher volatile mass fraction. It is also found that changes in primary particle size and particulate nanostructure are not directly proportional to the biodiesel content, while changes in particulate volatility and particulate oxidation reactivity are proportional to the biodiesel content. The use of biodiesel can enhance particulate oxidation reactivity and the regeneration of soot particles in an after-treatment device.