In a method of producing a glass substrate for a mask blank, a surface of the glass substrate is polished by the use of an alkaline polishing liquid that contains colloidal silica abrasive grains, from which alkali metal is removed to suppress occurrence of an alkali metal gel substance protrusion adhered on the glass substrate. The polishing process may include 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 may be followed by a protrusion suppressing step under a pressure lower than the predetermined pressure, to minimize polishing rate and suppress occurrence of a fine convex protrusion.