A method of manufacturing a semiconductor device includes forming a first through via surrounded by a liner in a first semiconductor substrate, first-recessing the semiconductor substrate to expose a first portion of the liner covering an end portion of the first through via, and forming a first diffusion barrier layer covering the first-recessed first semiconductor substrate and exposing a second portion of the liner. The method also includes removing the second portion of the liner and second-recessing the first diffusion barrier layer. The method further includes forming a second diffusion barrier layer that covers the second-recessed first diffusion barrier layer and a top portion of the liner from which the second portion is removed and exposes a top surface of the end portion of the first through via.