In a method and apparatus of aligning liquid crystal, a first ion beam is formed. The first ion beam is transformed into a second ion beam having transformed cross-section. The second ion beam advances toward a thin film including carbon-carbon double bond. The second ion beam forms a first angle with respect to the thin film. The second ion beam is transformed into an atomic beam. The atomic beam is irradiated onto the thin film to break the carbon-carbon double bond. The carbon-carbon double bond is broken to form a polarized functional group for aligning a liquid crystal molecule.