In this study, the electric storage effect of AlO6 clusters in amorphous alumina (AAO) supercapacitors was investigated in terms of cluster morphologies under electron-beam irradiation. Based on first-principles density functional calculation, the optimised structure of AlO6 clusters around an O-vacancy is characterised by a large vacant space created by the absence of an O atom and its neighbouring Al atom. The localised electrons present near the two-atomic vacancies induce positive charges on the inside of the insulating oxide surface, ensuring the adsorption of many electrons on the surface. Electron-beam irradiation (adsorption) from 100 to 180 keV causes the lengths of the Al–O bonds of the cluster to shrink, but then return to the original length with decreasing voltage energy, indicating a rocking-chair-type charge-breathing effect accompanied by a volume expansion of approximately 4%. The I–V and I–R characteristics depicted Coulomb blockade for the switching effect of both the negative and positive potentials. The Ragone plot of the AAO supercapacitor is located at capability area of the second cell.