A bonding apparatus for bonding substrates having metal bonding portions, includes: a processing container having an opening formed on the bottom of the processing container; a thermal treating plate disposed within the processing container, the thermal treating plate allowing for substrates to be mounted thereon and allowing for thermal treatment of the substrates; a pressing mechanism disposed within the processing container opposite the thermal treating plate and which presses the substrates to the thermal treating plate; an annular supporter which is disposed in an inner side of the processing container along the opening of the processing container, the annular supporter providing an airtight seal between the processing container and the thermal treating plate, and supporting the thermal treating plate; and a cooling mechanism which is disposed in an inner side of the supporter below the thermal treating plate, the cooling mechanism cooling the thermal treating plate.