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The liquid crystal (LC) alignment of molybdenum trioxide (MoO3) thin layers through ion-beam (IB) irradiation leads to LC alignment characteristics that are superior to those obtained with rubbed polyimide (PI) layers. We found that LC alignment states on a thin MoO3 layer are influenced by changes in IB irradiation energy. X-ray photoelectron spectroscopy analysis showed that the binding intensities of the Mo peaks that significantly decreased at IB irradiation energies greater than 2400 eV can homogeneously align with the LC and MoO3 molecules. An examination of the electro-optical characteristics revealed that MoO3 gave rise to a fast LC response time when compared to the PI layer.