A space needed to transfer a substrate container is decreased. A substrate processing apparatus includes a locating part where a substrate container accommodating a substrate is located; a driving unit configured to drive the locating part vertically; a transfer robot configured to transfer the substrate container; and a controller configured to control the driving unit and the transfer robot to move the locating part downward after the transfer robot moves to under the locating part to transfer the substrate container from the locating part to the transfer robot.