A substrate processing system configured to process a substrate includes a first modifying apparatus configured to form, in a combined substrate in which a front surface of a first substrate and a front surface of a second substrate are bonded to each other, an internal modification layer elongated within the first substrate in a plane direction from a center of the first substrate toward at least an edge portion of the first substrate as a removing target; a second modifying apparatus configured to form, within the first substrate, an edge modification layer elongated in a thickness direction of the first substrate along a boundary between the edge portion and a central portion of the first substrate; and a separating apparatus configured to separate a portion of the first substrate at a rear surface side, starting from the internal modification layer.