A method of manufacturing MOS transistor includes providing a substrate having a gate formed thereon; forming a hard mask layer on the substrate, performing an acid treatment to a surface of the hard mask layer, forming a photoresist layer on the hard mask layer after performing the acid treatment, performing a photolithography process to pattern the photoresist layer and the hard mask layer, performing an etching process to form recesses in the substrate, and performing a SEG method to form epitaxial layers respectively in the recesses.