A method for manufacturing a high quality semiconductor device having a through via structure. A substrate is manufactured with an oxide layer including a window region in a region in which a through via is formed. The substrate is bonded with another substrate to form an SOI substrate. The SOI substrate is ground to reduce its thickness. An island region is formed in a region at which a TSV (Through Silicon Via) structure is formed. A device and a TSV are coupled by a wire. The silicon substrate at a bottom side of the SOI substrate is removed to expose the island region from the bottom. A back contact for the TSV is formed in the window region, which is formed in a buried oxide layer.