A head alignment apparatus for determining a reference position using position synchronization and aligning a plurality of head modules according to the reference position, and a substrate treating system including the same are provided. The head alignment apparatus may include, a reference position determining unit for determining a first reference position of a head transfer, in which a plurality of inkjet head modules are installed; and a mounting position determining unit for determining a second reference position of the inkjet head module based on the first reference position so that the inkjet head module can be moved from a current position to a second reference position, wherein the reference position determining unit determines a first reference position using a first image sensor installed on the same plane as the inkjet head module and a second image sensor installed facing the inkjet head module.