A three-dimensional semiconductor device includes an upper substrate, a gate-stacked structure on the upper substrate, the gate-stacked structure including gate electrodes stacked within a memory cell array region, while being spaced apart from each other in a direction perpendicular to a surface of the upper substrate, and extending into an extension region adjacent to the memory cell array region to be arranged within the extension region to have a staircase shape, and at least one through region passing through the gate-stacked structure within the memory cell array region or the extension region, the at least one through region including a lower region and an upper region wider than the lower region.