A three-dimensional semiconductor device and a method of forming the same are provided. The three-dimensional semiconductor device comprises a substrate including first and second areas; first and second main separation patterns, disposed on the substrate and intersecting the first and second areas; gate electrodes disposed between the first and second main separation patterns and forming a stacked gate group, the gate electrodes sequentially stacked on the first area and extending in a direction from the first area to the second area; and at least one secondary separation pattern disposed on the second area, disposed between the first and second main separation patterns, and penetrating through the gate electrodes disposed on the second area. The gate electrodes include pad portions on the second area, and the pad portions are thicker than the gate electrodes disposed on the first area and in contact with the at least one secondary separation pattern.