A method of manufacturing a semiconductor device includes sequentially disposing a hard mask layer, an organic layer, and a metal-containing photoresist layer on a substrate, patterning the metal-containing photoresist layer to form a first mask pattern exposing a first region of the organic layer, implanting ions into the first region of the organic layer exposed by the first mask pattern, removing the first mask pattern and a second region of the organic layer that is not ion-implanted to form a second mask pattern exposing a partial region of the hard mask layer, and removing the partial region of the hard mask layer exposed by the second mask pattern to form a third mask pattern.