A bonding system includes a substrate transfer device configured to transfer a first substrate and a second substrate in a normal pressure atmosphere, a surface modifying apparatus configured to modify surfaces of the first substrate and the second substrate to be bonded with each other in a depressurized atmosphere, a load lock chamber in which the first substrate and the second substrate are delivered between the substrate transfer device and the surface modifying apparatus and in which an internal atmosphere of the load lock chamber is switchable between an atmospheric pressure atmosphere and the depressurized atmosphere, a surface hydrophilizing apparatus configured to hydrophilize the modified surfaces of the first substrate and the second substrate, and a bonding apparatus configured to bond the hydrophilized surfaces of the first substrate and the second substrate by an intermolecular force.