The thermal oxidation of Si(001) surface under 1000 K in the O 2 pressure of 1x10 - 4 Pa has been in situ investigated using real-time photoemission spectroscopy with high energy-resolution synchrotron radiation. Using a reaction kinetics model, we found that the oxidation at 1000 K progressed with a two dimensional island growth mechanism involving desorption of SiO molecules. Si 2 + species relating to the backbond oxidation at the topmost Si dimers appeared in conjunction with Si 1 + species at the initial oxidation stage at 1000 K. We clarified that the topmost Si atoms bonding to two oxygen atoms played an important role as an initial adsorbate. Since Si oxidation states with higher oxidation numbers, such as Si 4 + and Si 3 + , appeared at the early oxidation stages as well, we concluded that SiO 2 adsorbates constructed with the Si 4 + species were preferentially formed even in the oxide nucleus as well as the two dimensional islands on the Si(001) surface at 1000 K.