A bonding system includes a first holder and a second holder arranged to be spaced apart from each other in a vertical direction; a position adjuster configured to move the first holder and the second holder relatively to perform a position adjustment in a horizontal direction between a first substrate held by the first holder and a second substrate held by the second holder; a pressing unit configured to press the first substrate and the second substrate against each other; a measuring unit configured to measure a position deviation between an alignment mark on the first substrate and an alignment mark on the second substrate, the first substrate and the second substrate being bonded by the pressing unit; and a position adjustment controller configured to control the position adjustment in the horizontal direction in a currently-performed bonding processing based on the position deviation generated in a previously-performed bonding processing.