The possible models of the silicon oxide clusters on Si（001） surface, including the regular symmetric structure （A）, the periodic asymmetric structure （B）, the periodic asymmetric structure （C） and the irregular structure （D）, have been fully optimized using the first-principles general gradient approximation method based on density-functional theory. The results show that all the optimized surface structures are amorphous. The optimized surface structures of the B, C and D models have the similar geometric character as the tetrahedron structure of SiO2. Furthermore, the coalescence between the Si and O atoms of the silicon oxide clusters includes significant ionic bond and certain covalent bond as shown by employing the Mulliken population analysis and the graphics of electron localization function.