A bonding apparatus configured to bond substrates includes 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 rotator configured to rotate the first holder and the second holder relatively; a moving device configured to move the first holder and the second holder relatively in a horizontal direction; three position measurement devices disposed at the first holder or the second holder rotated by the rotator and configured to measure a position of the first holder or the second holder; and a controller configured to control the rotator and the moving device based on measurement results of the three position measurement devices.