A bypass route is provided in order to transfer a substrate without passing through the atmospheric pressure transfer chamber, that is, a loader module, from a load lock chamber to a storage. In the bypass route, a sub-transfer unit for transferring the processed substrate from the load lock chamber to the storage is provided. The sub-transfer unit transfers the processed substrate from the load lock chamber to the storage, and a main transfer unit of the loader module returns the processed substrate from the storage to a transport container on holding stage.