A method of manufacturing a CMOS device includes providing a substrate having a first region and a second region; forming a first gate structure and a second gate structure, each of the gate structures comprising a sacrificial layer and a hard mask layer; forming a patterned first protecting layer covering the first region and a first spacer on sidewalls of the second gate structure; performing an etching process to form first recesses in the substrate; performing a SEG process to form epitaxial silicon layers in each first recess; forming a patterned second protecting layer covering the second region; and performing a dry etching process with the patterned second protecting layer serving as an etching mask to etch back the patterned first protecting layer to form a second spacer on sidewalls of the first gate structure and to thin down the hard mask layer on the first gate structure.