A method of fabricating a MOS transistor includes the steps of: providing a substrate; forming a gate structure on the substrate; forming a first spacer on the sidewall of the gate structure and forming at least a recess within the substrate next to the first spacer; performing an oxygen-containing process to form an oxygen-containing layer on the surface of the recess; performing a cleaning process to remove the oxygen-containing layer; performing an epitaxial process to form an epitaxial layer in the recess; and removing the first spacer.