We investigated the liquid crystal (LC) alignment on SiOx film surfaces as a function of ion beam exposure time using scanning probe microscopy and X‐ray photoemission spectroscopy. It was concluded that the LC alignment with high or low pretilt angles did not contribute to the morphological roughness but depended on the roughness in the electric potential of the SiOx surfaces. We also found that SiOx films with vertical LC alignment show relatively low values of stoichiometry parameters (1.42 < x < 1.57), whereas those with homogeneous LC alignment show relatively high values of stoichiometry parameters (1.58 < x < 1.77). All the experimental results showed that the electric dipole–dipole interactions between the LC molecules and the SiOx surfaces played a dominant role in aligning LC molecules on ion‐beam‐treated inorganic surfaces. Copyright © 2012 John Wiley & Sons, Ltd.