Graphene thin films are grown on Si substrates covered by SiO2 layers (SiO2/Si) with the method of directly depositing carbon atoms in the molecular beam epitaxy (MBE) equipment. The structural properties of the samples produced at different substrate temperatures (500℃, 600℃, 900℃, 1100℃, 1200℃) are investigated by Raman spectroscopy (Raman) and near-edge x-ray absorption fine structure (NEXAFS). The results indicate that the thin films grown at lower temperatures are amorphous carbon thin films. While the thin films grown above 700℃ exhibi the characteristics of graphene. As the substrate temperature increases, the crystalline quality of graphene is improved. However, very high temperature can reduce the quality of grapheme. The best graphene films are obtained at a substrate temperature of 1100℃. When the substrate temperature is low, the activity of the carbon atoms is not enough to form the ordered six member rings of C-sp2. While the substrate temperature is too high, the decomposition of some SiO2 induces the deposited carbon atoms to bond with decomposed oxygen atoms or silicon atoms, resulting in the defects on the surface, which leads to the poor crystalline quality of graphene films.