A bonding apparatus includes a first holder, a first transforming device, a second holder, a second transforming device, a suction device and a control device. The first holder attracts and holds a first substrate from above. The first transforming device transforms the first substrate held by the first holder such that a central portion of the first substrate is protruded downwards. The second holder is provided under the first holder, and attracts and holds a second substrate, which is to be bonded to the first substrate, from below. The second transforming device transforms the second substrate held by the second holder such that a central portion of the second substrate is protruded upwards. The suction device generates different attracting forces in multiple division regions included in an attraction region of the second substrate. The control device controls the suction device.