A room temperature bonding apparatus includes a first beam source, a second beam source, and a press bonding mechanism. The first beam source emits a first activation beam that irradiates a first surface of a first substrate. Independently from the first beam source, the second beam source emits a second activation beam that irradiates a second surface of a second substrate. The press bonding mechanism bonds between the first substrate and the second substrate by contacting between the first surface and the second surface after the first surface is irradiated with the first activation beam and the second surface is irradiated with the second activation beam. Thus, a plurality of the substrates made of different materials is appropriately bonded.