It is very important to characterize the depth change in chemical bonding structures of ultra-thin SiO2 films. The LO mode and the lower frequency shoulder peak of SiO2 on Si was detected by the FT-IR-ATR method, and this band was simulated by a gradient layered and effective medium model. Interface roughness estimated from the shoulder bands of ATR spectra was in good agreement with the GIXR results, and the shoulder band also reflects the change of Si-O-Si bonding angle. In our calculation, the shoulder band around 1150-1050 cm(-1) reflects the interface roughness and the shoulder band around 1250-1150 cm(-1) includes information about the change of Si-O-Si bonding angle and/or Si-O force constant. The FT-IR-ATR method is a useful technique with which to characterize SiO2 ultra-thin films.