A method of manufacturing a semiconductor device includes the steps of forming a plurality of first integrated circuits on the surface side of a first semiconductor substrate; forming a plurality of second integrated circuits in a semiconductor layer that is formed on a release layer provided on a second semiconductor substrate; bonding the two semiconductor substrates so that electrically bonding portions are bonded to each other to form a bonded structure; separating the second semiconductor substrate from the bonded structure at the release layer to transfer, to the first semiconductor substrate, the semiconductor layer in which the plurality of second integrated circuits are formed; and dicing the first semiconductor substrate to obtain stacked chips each including the first integrated circuit and the second integrated circuit.