The effect of liquid crystal (LC) alignment on a homeotropic polyimide (PI) surface induced by ion beam (IB) irradiation and rubbing process was studied. LC alignment was not affected by IB irradiation with an exposure time of 10 s, and an IB irradiation with an exposure time of 60 s more effectively oriented the LCs on the PI layer than the rubbing process. It was assumed that the LC alignment depended on the C-O bonds created from the C=O bonds on the PI surface broken by IB irradiation after an exposure time of 60 s, which resulted in a strong surface energy that transformed the homeotropic LC alignment to homogeneous states.