A controlling method for a wafer transportation part and a load port part on an EFEM includes a fixing step of fixing a container on an installation stand of the load port part, a first cleaning step of connecting a bottom nozzle of the load port part to multiple bottom holes formed on a bottom surface of the container and introducing a cleaning gas into the container and discharging a gas from the container via the nozzle, a connection step of connecting the container and the transportation room, and a wafer transportation step of transporting the wafer from the container to a processing room via the opening and the transportation room and transporting the wafer from the processing room to the container via the transportation room and the opening.