A method of manufacturing a semiconductor device having a vertical channel structure is provided. The method includes: (a) forming a stacked structure by alternately stacking interlayer insulating layers and sacrificial layers n times on a substrate; (b) forming a mask pattern on that stacked structure; (c) selectively etching the nth interlayer insulate layer as the uppermost interlayer insulating lay of the stacked structure by using the mask pattern as an etching mask; (d) selectively etching the nth sacrificial layer as the uppermost sacrificial lay of the stacked structure by using the mask pattern as an etching mask; (e) etching the sidewalls of the mask pattern; (f) selectively etching a plurality of interlayer insulating layers by using the etched mask pattern as an etching mask; (g) selectively etching a plurality of sacrificial layers by using the etched mask pattern as an etching mask; and (h) forming a ladder structure by repeating operations (e) to (g). Perforation defectsof the semiconductor device can be prevented and process cost can be reduced by reducing the number of photolithography processes.