In a method of producing a glass substrate for a mask blank, a surface of the glass substrate is polished by the use of a polishing liquid having a pH value between 7.0 and 7.6 that contains abrasive grains, and the abrasive grains include colloidal silica abrasive grains produced by hydrolysis of an organosilicon compound. The polishing process includes a surface roughness control step for initially finishing the surface of the glass substrate to a predetermined surface roughness by moving a polishing member and the glass substrate relative to each other under a predetermined pressure. This is followed by a protrusion suppressing step, carried out immediately before the end of the polishing process, under a pressure lower than the predetermined pressure, to minimize polishing rate and suppress occurrence of a fine convex protrusion. A mask blank and then a transfer mask are formed from this polished glass substrate.