Disclosed is a method of manufacturing a semiconductor device, including: forming a stacked structure including a plurality of layers, the stacked structure including a cell region, and first and second contact regions; forming a first mask pattern covering the cell region and the second contact region of the stacked structure; forming steps of n layers at a boundary of the cell region and the first contact region, where n is a natural number greater than or equal to 1; forming a second mask pattern on the stacked structure, wherein the second mask pattern covers the cell region and the formed steps and is expanded to partially cover the first and second contact regions; and etching the stacked structure by k layers by using the second mask pattern as an etch barrier, where k is a natural number greater than or equal to 2.