A method of controlling a laser beam annealing apparatus to manufacture a thin film transistor substrate, the method including: irradiating a laser beam emitted from a laser beam irradiator onto an amorphous silicon layer on a substrate supported by a substrate support; obtaining photographic data with respect to at least a part of the substrate by using a photographic unit; and adjusting a position of at least one of the substrate support or the laser beam irradiator by using a position adjuster based on the photographic data obtained by the photographic unit.