A method of manufacturing a semiconductor device is provided. The method includes transferring an internal shot and an external shot by performing a patterning process on a first wafer, analyzing an overlay of the first wafer, and performing a lithography process on a second wafer, based on the analyzing of the overlay of the first wafer, wherein the analyzing of the overlay of the first wafer includes providing, to the first region, first augmented overlays generated based on an orthogonal coordinate system using first and second directions perpendicular to each other as an axis, and providing, to the second region, second augmented overlays that are overlays in a radial direction from the center of the first wafer.