A lithography apparatus for substrate patterning, includes a substrate stage having a reference mark, an optical system irradiating the substrate with the charged particle beam, a first measurement device measuring a position of an alignment mark formed on the substrate, a second measurement device having an optical axis apart from an axis of the optical system by a distance shorter than that of the first measurement device, and measuring a position of the reference mark, a processor obtaining a base line of the first measurement device based on positions of the reference mark respectively measured by the first and second measurement device and a base line of the second measurement device, the position of the reference mark being measured by the second measurement device based on an optical signal obtained via the reference mark with the stage moved.