A method and an apparatus for bonding semiconductor substrates are provided. The method includes at least the following steps. A first position of a first semiconductor substrate on a first support is gauged by a gauging component embedded in the first support and a first sensor facing towards the gauging component. A second semiconductor substrate is transferred to a position above the first semiconductor substrate by a second support. A second position of the second semiconductor substrate is gauged by a second sensor mounted on the second support and located above the first support. The first semiconductor substrate is positioned based on the second position of the second semiconductor substrate. The second semiconductor substrate is bonded to the first semiconductor substrate.