A method of manufacturing a semiconductor device includes forming a cell chip including a first substrate, a source layer on the first substrate, a stacked structure on the source layer, and a channel layer passing through the stacked structure and coupled to the source layer, flipping the cell chip, exposing a rear surface of the source layer by removing the first substrate from the cell chip, performing surface treatment on the rear surface of the source layer to reduce a resistance of the source layer, forming a peripheral circuit chip including a second substrate and a circuit on the second substrate, and bonding the cell chip including the source layer with a reduced resistance to the peripheral circuit chip.