A method of manufacturing semiconductor device is provided. A substrate at least with a patterned silicon-containing layer on the substrate and spacers adjacent to the patterned silicon-containing layer is provided. A metal layer is formed on the substrate and covers the patterned silicon-containing layer and spacers. Then, a capping layer is formed on the metal layer. A first rapid thermal process is performed to at least make a portion of the metal layer react with the substrate around the spacers to form transitional silicides. The capping layer and the unreacted portions of the metal layer are removed. A first nitride film with a first tensile stress S1 is formed on the substrate. A second rapid thermal process is performed to transfer the transitional silicide to a silicide and transfer the first nitride film to a second nitride film with a second tensile stress S2, wherein S2>S1.