The mechanism of liquid crystal (LC) alignment has been investigated during the last few decades for inorganic materials as well as for organic materials; however, it has not been clearly confirmed for some alignment materials. Inorganic alignment materials such as amorphous silicon oxide (a-SiOx) and hydrogenated amorphous silicon oxide (a-SiOx:H) are deposited on indium tin oxide (ITO) films on glass by reactive sputtering deposition. After deposition, the inorganic alignment materials are irradiated using an Ar+ ion beam (IB) for LC alignment. On the basis of the experimental results, a-SiOx films deposited by the sputtering do not align the LC, but a-SiOx:H films treated with varying IB energies, IB incident angles, IB doses, and IB irradiation times have excellent alignment properties and electrooptical properties, identical to those of polyimide (PI). These results imply that inorganic alignment layers irradiated by IB can be adopted as an LC alignment layer instead of rubbed PI. Additionally, hydrogen plays an important role in LC alignment because of the difference in alignment properties between a-SiOx films and a-SiOx:H films. We investigate the mechanism of IB-treated inorganic alignment layers and suggest that LCs are aligned by chemical effects, such as van der Waals interaction, more than by physical effects, such as morphology effects, in the inorganic alignment layer irradiated by IB.