A method of fabricating a semiconductor device is provided. The method includes forming a refractory metal alloy layer over a silicon-containing conductive layer. The refractory metal alloy layer is constituted of a first refractory metal and a second refractory metal. Thereafter, a cap layer is formed on the refractory metal alloy layer. A thermal process is performed so that the refractory metal alloy layer reacts with silicon of the silicon-containing conductive layer to form a refractory metal alloy salicide layer. Afterwards, an etch process with an etch solution is performed to removes the cap layer and the refractory metal alloy layer which has not been reacted and to form a protection layer on the refractory metal alloy salicide layer.