A method of manufacturing a semiconductor device includes: forming a gate over a semiconductor substrate; forming doped regions in the semiconductor substrate on both sides of the gate; depositing a dielectric layer on sidewalls of the gate; depositing a spacer laterally surrounding the dielectric layer, the spacer including a carbon-free portion and a carbon-containing portion laterally surrounding the carbon-free portion; removing the gate and vertical portions of the dielectric layer to form a recess; and filling a conductive layer in the recess.