A method of manufacturing a semiconductor device includes: providing a substrate; forming a gate structure on the substrate; depositing a first dielectric layer over the gate structure; depositing a conductive interconnect in a trench of the first dielectric layer thereby exposing a surface of the conductive interconnect through the first dielectric layer; depositing a conductive layer over the exposed surface of the conductive interconnect; depositing a silicon-containing layer over the conductive layer and the conductive interconnect; and forming a metal silicide layer to be a silicide form of the conductive layer by reacting the conductive layer with silicon in the silicon-containing layer.