A method of manufacturing a semiconductor device includes: forming a first patterned stack structure including a cell region, a first portion in a first contact region, and a second portion in a second contact region, the second portion of the first patterned stack structure including a first opening; forming a second patterned stack structure including a third portion over the cell region and the second contact region of the first patterned stack structure; forming a second opening penetrating the third portion of the second patterned stack structure, the second opening being coupled to the first opening; and forming a third opening penetrating the first portion of the first patterned stack structure when the second opening is formed.