The ReaxFF molecular dynamics simulations, which can predict chemical reactions, were performed on integral asphalt and individual asphalt molecules at different temperatures and oxygen levels to investigate the oxidation mechanism of asphalt and develop a molecular model suitable for aged asphalt. The simulation of integral asphalt suggests that the main oxidation products of asphalt are C-O, H-O, and S-O bonds. The oxygen level has the greatest influence on the yield of C-O bonds, and the temperature has the greatest influence on the H-O bonds. The simulation of individual asphalt molecules indicated that the oxidation of asphalt is accompanied by the decomposition of the aromatic rings, and thus, the aromaticity of the oxidized asphalt is decreased. Oxidation of asphaltenes starts with the oxygen molecules attacking the aromatic ring and generating a ketone, while the initial reactions of the other components are diverse. In addition, the simulation results were validated with Fourier transform infrared spectroscopy and nuclear magnetic resonance tests and were used to study the effects of oxidation on the characteristics of asphalt. The results suggested that the introduction of oxygen-containing functional groups decreases the component compatibility of asphalt and causes the aged asphalt to be harder and more viscous.