A substrate processing apparatus has a transfer mechanism arranged on a transfer base and configured to transfer a processing substrate between predetermined transfer positions, a mapping sensor arranged on the transfer base and configured to detect an arrangement state of a processing substrate inside a processing substrate accommodating case which accommodates a plurality of processing substrate in a shelf-like form, and a Z-axis teaching jig provided on or in the vicinity of one of the transfer positions. This substrate processing apparatus detects, by the mapping sensor, a height of the Z-axis teaching jig so as to perform teaching of Z-axis to the transfer mechanism with respect to the one of the transfer positions.