A lithography apparatus for performing pattern formation on a substrate includes a stage configured to hold the substrate and be movable, an optical system configured to irradiate the substrate with an energy beam for the pattern formation, and a controller configured to set an arrangement of first and second marks for overlay inspection, which is variable with respect to a first substrate for condition setting, and control the stage and the optical system so that first processing for forming the first mark on the first substrate without the pattern formation and second processing for forming the second mark on the first substrate with the pattern formation are performed based on the set arrangement.