Large-scale modeling of a SiO2/Si(001) structure including a couple of monoatomic steps has been performed by using a novel inter-atomic potential energy function for Si, O mixed systems. The SiO2 film was formed by layer-by-layer insertion of O atoms into Si-Si bonds of Si(001) 2 x 1 reconstructed surface misoriented from surface normal by 3.2 degrees. Just after the backbond oxidation of the dimer structures, a clear difference in the structural order of oxide films appeared between two types of terraces on which the dimer rows run perpendicular and parallel to the step lines. The difference is explained by the difference in stretching directions of Si-Si intervals into which O atoms are inserted. It was also found that the oxide structure near the step preferentially became amorphous after further oxidation. These results suggest a possibility that the structure of thin oxide film can be controlled by the initial Si surface preparation.