A bonding apparatus includes a first holder, a second holder, an attracting pressure generator and a lift pin. The first holder is configured to hold a first substrate. The second holder, disposed at a position facing the first holder, has an attraction surface configured to attract a second substrate to be bonded to the first substrate. The attracting pressure generator is configured to generate an attracting pressure in the attraction surface. The lift pin is configured to space the second substrate on the attraction surface apart from the second holder. The second holder is provided with a space including an opening through which the lift pin passes, and the space is controlled to have a pressure lower than an atmospheric pressure.