A method of manufacturing a semiconductor device, comprising the steps of preparing a structure including a semiconductor substrate, an element formed therein, a through hole formed to penetrate the semiconductor substrate, and an insulating layer formed on both surface sides of the semiconductor substrate and an inner surface of the through hole, and covering the element, forming a penetrating electrode in the through hole, forming a first barrier metal pattern layer covering the penetrating electrode, forming a contact hole reaching a connection portion of the element in the insulating layer, removing a natural oxide film on the connection portion of the element in the contact hole, and forming a wiring layer connected to the first barrier metal pattern layer and connected to the element through the contact hole.