We apply a first-principles molecular-dynamics method based on the density functional theory to calculate several initial configurations of an O2 molecule adsorbed on a Si(001) surface. The bonding processing, adsorption energy, dynamic track, and diffusion coefficient are investigated. The results indicate that the adsorption process may be divided into four stages: physical adsorption, chemical adsorption early stage, chemical adsorption late stage, and the superficial stable state. The Si=O structure, the Si–O–Si surface oxygen-bridge structure, and the Si–O–Si oxygen-bridge structure where oxygen atoms are inserted into the backbonds between the surface and the second layer of silicon atoms in the stable adsorption structures, are beneficial to the formation of the silica tetrahedral structure. We conclude that the remarkable difference between the diffusion coefficients during the physical adsorption stage leads to different diffusion paths, which results in the formation of two concomitant stable structures in the early process of silicon surface oxidation.