A method for setting a substrate processing apparatus having a head for dispensing ink includes aligning a position of at least one vision unit, by moving the vision unit above a reference mark and taking, by the vision unit, an image of the reference mark, in which the vision unit takes an image of a substrate, and the reference mark is made on the substrate processing apparatus and fixed in one position, and aligning at least one of a movement axis of the vision unit, a position of the substrate, or a movement axis of the substrate, by moving the vision unit or the substrate in a state in which the substrate having alignment marks made thereon is located under the vision unit and taking, by the vision unit, an image of the alignment marks.