Sequential high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) was used to clarify the detailed process of structural changes in Au/CeO2 catalysts found in our previous TEM observations. The layer-by-layer shrinkage of a Au nanoparticle on CeO2 during electron beam irradiation and recovery at the same position after switching off the beam were observed with clear resolution of Ce and Au atomic columns. Displaced Au atomic columns at the perimeter of the Au/CeO2 interface during the electron beam irradiation have been analyzed using first-principles calculations, which indicate that such Au atoms at the perimeter edge are located above oxygen vacancies or Ce-terminated surface regions. The present behavior of Au atoms and nanoparticles provides valuable insights into the mechanisms of both structural changes and catalytic activity of Au/CeO2 catalysts.