A method of manufacturing a complementary metal-oxide semiconductor (CMOS) transistor includes: forming a semiconductor layer in which an n-MOS transistor region and a p-MOS transistor region are defined; forming an insulation layer on the semiconductor layer; forming a conductive layer on the insulation layer; forming a mask pattern exposing the n-MOS transistor region, on the conductive layer; generating a damage region in an upper portion of the conductive layer by implanting impurities in the conductive layer of the n-MOS transistor region using the mask pattern as a mask; removing the mask pattern; removing the damage region; and patterning the conductive layer to form an n-MOS transistor gate and a p-MOS transistor gate. Accordingly, gate thinning and formation of a step between the n-MOS transistor region gate and the p-MOS transistor region gate can be prevented.