A method for fabricating a semiconductor device includes forming a first semiconductor wafer, in which a circuit part and a first bonding layer are stacked, on a first semiconductor substrate, forming a second semiconductor wafer, which includes structures and an insulating layer for gap-filling between the structures, on a second semiconductor substrate, the structures including a pillar and bit lines stacked therein, bonding the first semiconductor wafer with the second semiconductor wafer so that the first bonding layer faces the insulating layer, and separating the second semiconductor substrate from the bonded second semiconductor wafer.