A semiconductor device has a high electric connection reliability and includes a base substrate having a connection target layer, a lower contact plug formed over the base substrate and electrically connected to the connection target layer, and an upper contact plug formed over the lower contact plug, wherein the lower contact plug includes a lower plug layer having a gap portion extending inward from a top portion of the lower plug layer, a gap cover layer filling the gap portion, and an upper cover layer covering a top surface of the lower plug layer.