A method of manufacturing a semiconductor device includes forming a first masking layer and second masking layer over a substrate. The first masking layer includes an opening over an active area and a spacer in the substrate, and the second masking layer blocks a portion of the opening in the first masking layer. The method includes performing an etching process, using the first masking layer and the second masking layer as an etching mask, to form a contact opening which exposes a portion of the active area and a portion of the spacer, and forming a contact plug in the contact opening and over the exposed portion of the active area and the exposed portion of the spacer.