When a substrate is transferred by a holding arm to a multiple tier wafer boat, contact between the holding arm and the substrate is prevented. When the wafer boat is not subjected to a thermal effect, a normal height position of a ring member is obtained by relatively elevating and lowering a transfer base member with respect to the wafer boat. Before a wafer, which is not yet thermally processed, is transferred to the wafer boat, a height position of the corresponding ring member is obtained. By comparing a difference between the normal height position of the ring member and the height position of the ring member before the wafer is transported, with a threshold value, whether to transfer the wafer by the wafer transfer mechanism to the wafer boat can be judged.