A method performed by a film deposition apparatus includes supplying a first reaction gas, which is adsorbable to hydroxyl groups, to a surface of a substrate and causing the first reaction gas to be adsorbed onto the surface of the substrate; supplying a second reaction gas to the substrate and causing the second reaction gas to react with the first reaction gas adsorbed onto the surface of the substrate to form a reaction product on the substrate; supplying an activated third reaction gas to the substrate to modify a surface of the reaction product; and supplying a fourth reaction gas including a hydrogen-containing gas to at least a partial area of the modified surface of the reaction product to form hydroxyl groups on at least the partial area.