A batch forming apparatus forms a batch of substrates by combining a plurality of substrates that have been taken out from a plurality of carriers each containing therein the substrates in a stacked manner. The batch forming apparatus includes: a substrate transfer mechanism that takes out the substrates from each carrier and transfer the substrates; a substrate relative positional relationship changing mechanism that rearranges one or more substrates out of the substrates transferred by the substrate transfer mechanism one by one relative to other substrates to change positional relationships of the substrates relative to each other; and a batch forming mechanism that forms a batch of substrates out of the substrates that have been transferred thereto by the substrate transfer mechanism, with positional relationships of the substrates having been changed relative to each other by the substrate relative positional relationship changing mechanism. A substrate processing system includes such a batch forming apparatus, and a substrate processing apparatus that process the batch of substrates formed by the batch forming apparatus.