A method of manufacturing a semiconductor device includes forming a first etch stop pattern on a lower structure including a first region and a second region to expose the second region, stacking a plurality of stack structures on the lower structure to overlap the second region and the first etch stop pattern, forming a stepped stack structure by etching the plurality of stack structures to expose an end portion of the first etch stop pattern, forming a slit passing through the stepped stack structure and the first etch stop pattern, and replacing sacrificial layers of the plurality of stack structures and the first etch stop pattern with conductive patterns through the slit.