A three-dimensional semiconductor device may include a substrate having a cell area and an extension area, a word line stack disposed above the substrate, the word line stack including mold layers and word lines alternately stacked, vertical channel structures vertically penetrating the word line stack in the cell area, and a first extension through-via structure vertically penetrating the word line stack in the extension area. The first extension through-via structure may include a first via plug and a first via liner layer surrounding sidewalls of the first via plug. The first via liner layer may include first dents respectively disposed at the same levels horizontally as the word lines of the word line stack.