A three-dimensional semiconductor device includes a plurality of stack structures extending in one direction on a substrate and spaced apart from each other, a plurality of vertical structures penetrating the stack structures, a common source plug between the stack structures that are adjacent to each other and extending in parallel to the stack structures, and a spacer structure at each side of the common source plug. The stack structure has a sidewall defining recess regions vertically spaced apart from each other. The spacer structure covers sidewalls of the stack structures. The spacer structure includes an insulating spacer and a protection spacer. The insulating spacer fills the recess regions of the stack structure and includes a surface having grooves. The protection spacer fills the grooves of the surface of the insulating spacer and has a substantially flat surface.