We investigated the correlations between the surface energy and the tilt angle on homeotropic polyimide (PI) surfaces subjected to rubbing using ion beam (IB) irradiation. The tilt angle of nematic liquid crystal (NLC) decreased with increased rubbing times. Also, the tilt angle of NLC was measured to be homeotropically aligned and then rapidly changed to homogeneous alignment with increasing IB irradiation time. We assumed that the LC alignment depends strongly on the C-O bonds created from C = O bonds on the PI surface broken with IB irradiation, which was confirmed through X-ray photoelectron spectroscopy measurements. In addition, the contact angle on the PI surface decreased with increasing IB irradiation time. Therefore, we conclude that the IB irradiation is attributed to the high surface energy and the compositional variation of the homeotropic PI, resulting in a transition of NLC orientation.