A bonding apparatus configured to bond substrates comprises a first holder configured to vacuum-exhaust a first substrate to attract and hold the first substrate on a bottom surface thereof; a second holder disposed under the first holder, and configured to vacuum-exhaust a second substrate to attract and hold the second substrate on a top surface thereof; a mover configured to move the first holder and the second holder relatively in a horizontal direction; a laser interferometer system configured to measure a position of the first holder or the second holder which is moved by the mover; a linear scale configured to measure a position of the mover; and a controller configured to control the mover based on a measurement result of the laser interferometer system and a measurement result of the liner scale.