Cross-section transmission electron microscopy (TEM) was used to study SnOx thin films that were deposited at room temperature on Si using electron beam evaporation and subsequently treated by oxygen plasma. Electron diffraction and high-resolution TEM studies show that the as-deposited SnOx thin films are composed of amorphous and nanocrystalline SnO2 structures with a size ranged from 5 to 8 nm in diameter. Long-time (>6 min) O-plasma-treated thin films are composed of sub-nanometer cluster structures. The thin films that were oxygen-plasma-treated for a short period of time (<6 min) consist of a two-layered structure composed of a sub-nanometer cluster layer and a nanocrystalline SnO/white Sn layer. The structural evolution of the SnO2 thin films during the O-plasma processing is discussed.