A room-temperature bonding apparatus comprising: a vacuum chamber; a first holding mechanism disposed in said vacuum chamber to hold a first substrate; a second holding mechanism disposed in said vacuum chamber to hold a second substrate; a target holding mechanism disposed in said vacuum chamber to hold at least one target (7;11-15); a beam source disposed in said vacuum chamber to irradiate an activation beam to a bonding surface of the first substrate and a bonding surface of the second substrate and to the exposed area of said target holding mechanism, wherein said beam source is one that generates a fast atom beam; a pressure bonding mechanism disposed in said vacuum chamber to bond the first and second substrates such that the bonding surface of the first and second substrates irradiated with the activation beam are opposed to each other, and a covering member covering the inner surface of said vacuum chamber, wherein said covering member is disposed to be detachable or exchangeable from said vacuum chamber and is formed of a first material, wherein said target holding mechanism has a plurality of areas in which a plurality of said targets (7,12-14) or pseudo targets (11, 15) of the first material can be arranged, wherein a pseudo target of the first material is arranged in at least one of the plurality of areas, wherein, when the first substrate is a silicon substrate, the first material comprises silicon or silicon oxide as main component, or, when the first substrate is a sapphire substrate, the first material comprises aluminum or aluminum oxide as main component, or, when the targets (7, 12-14) are formed of metal materials, the first material is an insulator like silicon oxide or aluminum oxide, or ceramic material, or yttrium, or tungsten. a vacuum chamber; a first holding mechanism disposed in said vacuum chamber to hold a first substrate; a second holding mechanism disposed in said vacuum chamber to hold a second substrate; a target holding mechanism disposed in said vacuum chamber to hold at least one target (7;11-15); a beam source disposed in said vacuum chamber to irradiate an activation beam to a bonding surface of the first substrate and a bonding surface of the second substrate and to the exposed area of said target holding mechanism, wherein said beam source is one that generates a fast atom beam; a pressure bonding mechanism disposed in said vacuum chamber to bond the first and second substrates such that the bonding surface of the first and second substrates irradiated with the activation beam are opposed to each other, and a covering member covering the inner surface of said vacuum chamber, wherein said covering member is disposed to be detachable or exchangeable from said vacuum chamber and is formed of a first material, wherein said target holding mechanism has a plurality of areas in which a plurality of said targets (7,12-14) or pseudo targets (11, 15) of the first material can be arranged, wherein a pseudo target of the first material is arranged in at least one of the plurality of areas, wherein, when the first substrate is a silicon substrate, the first material comprises silicon or silicon oxide as main component, or, when the first substrate is a sapphire substrate, the first material comprises aluminum or aluminum oxide as main component, or, when the targets (7, 12-14) are formed of metal materials, the first material is an insulator like silicon oxide or aluminum oxide, or ceramic material, or yttrium, or tungsten.