A manufacturing method of a semiconductor device includes generating hydrogen radicals by plasma excitation of hydrogen gas and exposing a surface of a substrate on which silicon and metal are exposed to a reducing atmosphere created with the hydrogen radicals, and generating hydrogen radicals and hydroxyl radicals by plasma excitation of a mixed gas of hydrogen gas and oxygen-containing gas and oxidizing the silicon exposed on the surface of the substrate by exposing the surface of the substrate to the hydrogen radicals and hydroxyl radicals to obtain the substrate on which the metal and oxidized silicon are formed.