There is provided a substrate processing apparatus, including: a mounting part on which a carrier having a plurality of slots capable of accommodating a plurality of substrates is mounted; a transfer part configured to load and unload the substrates to and from the plurality of slots based on a reference accommodation position set in the mounting part; a detection part configured to detect a position of each of the plurality of substrates accommodated in the plurality of slots; and a correction part configured to correct the reference accommodation position based on port accumulation information in which detection results obtained by the detection part from a plurality of carriers which has been mounted on the mounting part in the past are accumulated.