In a method of manufacturing a semiconductor device, a first substrate and a second substrate, which include a plurality of memory cells and selection transistors, respectively, are provided. A first insulating interlayer and a second insulating interlayer are formed on the first substrate and the second substrate, respectively, to cover the memory cells and the selection transistors. A lower surface of the second substrate is partially removed to reduce a thickness of the second substrate. The lower surface of the second substrate is attached to the first insulating interlayer. Plugs are formed through the second insulating interlayer, the second substrate and the first insulating interlayer to electrically connect the selection transistors in the first substrate and the second substrate to the plugs. Thus, impurity ions in the first substrate will not diffuse during a thermal treatment process.