A semiconductor device includes a first substrate in which a first region and a second region are defined, a first stack structure with first gate electrodes displaced and stacked sequentially on the first substrate, a second stack structure with second gate electrodes displaced and stacked sequentially on the first stack structure, a junction layer disposed between the first stack structure and the second stack structure, a first interlayer insulating layer disposed on a side surface of the first stack structure, a second interlayer insulating layer covering the second stack structure, a first channel hole that penetrates through structure(s) and/or layer(s) and a second channel hole that penetrates through structure(s) and/or layer(s). A height of the second portion of the first channel hole in a second direction orthogonal to the first direction is less than a height of the second portion of the second channel hole in the second direction.