The influence of oxidative aging on the structure and thermodynamic properties of biodiesel was investigated using molecular dynamics simulation at the micro-scale. The oxidative aging biodiesel models were constructed by incorporating the oxidative aging products including the primary oxidation products, decomposition products, and oligomers. The competitive effects between the decomposition reaction and the polymerization reaction were also considered. The temperature dependent behaviors of density, cohesive energy density, solubility parameter, self-diffusion coefficients, hydrogen bonds, and shear viscosity were analyzed to gain insights into the molecular dynamics after oxidative aging. The simulation results indicate that the decomposition of biodiesel molecules promotes the formation of polar groups and low molecular weight molecules, enhancing the intermolecular interactions and molecule mobility, respectively. Nevertheless, a higher concentration of decomposition products results in a decrease in both shear viscosity and activation energy. Moreover, the formation of oligomers contributes to an increase in both shear viscosity and activation energy, while causing a decrease in molecular mobility, due to the long hydrocarbon chains and molecule aggregation. The complicated changes of properties are strongly dependent on interaction energy and molecular structures deriving from the synergism behavior of the different oxidative aging products.