A substrate bonding system in one manner of the present disclosure includes a surface treatment module configured to perform plasma processing on a surface of a substrate. The substrate bonding system includes a deposition module coupled to the surface treatment module such that the substrate is transferred to the deposition module without being exposed to atmosphere, the deposition module being configured to perform a deposition process on the substrate on which the plasma processing is performed in the surface treatment module. The substrate bonding system includes a bonding module coupled to the deposition module such that the substrate is transferred to the bonding module without exposing the substrate to the atmosphere, the bonding module being configured to bond substrates on which the deposition process is performed in the deposition module, to form a bonded body.