An overlay correcting method capable of optimizing correction of an overlay within a scanner correction limit of a scanner of a scanner system, and a photolithography method, a semiconductor device manufacturing method and the scanner system which are based on the overlay correcting method are provided. The overlay correcting method includes collecting overlay data by measuring an overlay of a pattern; calculating correction parameters of the overlay by performing regularized regression using the overlay data, the regularized regression being based on a correction limit of the scanner such that the correction parameters fall within the correction limit of the scanner; and providing the correction parameters to the scanner.