A bonding system and a bonding method for alignment are provided. An optical semiconductor includes a light source and a plurality of protruded elements on a surface thereof. A semiconductor bench includes a light receiving element and a plurality of recess elements on a surface thereof. A sidewall of the protruded elements or a sidewall of the recess elements is slanted. A first metallized layer is disposed on a bonding surface of each protruded element and a second metallized layer is disposed on a bottom surface of each recess element, wherein the first metallized layer is used for bonding with the second metallized layer.