The invention provides a semiconductor device and manufacturing method thereof, which is able to improve manufacturing yield of the semiconductor device having a plurality of semiconductor chips overlapped in three-dimensional. A penetration electrode (17) reaching a pad (3) from a second surface of a semiconductor substrate (1) is formed. A penetration space in the penetration electrode (17) is formed of a first hole (7) and a second hole (11) with a diameter smaller than that of the first hole (7). The first hole (7) is formed from the second surface (1b) of the semiconductor substrate (1) to the middle of the interlayer insulating film (2). Further, the second hole (11) reaching the pad (3) from the bottom of the first hole (7) is formed. Then, the interlayer insulating film (2) formed on the first surface(1a) of the semiconductor substrate (1) has a step shape reflecting a step difference between the bottom surface of the first hole and the first surface of the semiconductor substrate. More specifically, the thickness of the interlayer insulating film between the bottom surface of the first hole and the pad is smaller than that in other portions.