The substrate processing apparatus 1b roughly consists of a first carrier placing unit 2b, a substrate processing unit 3b, and a second carrier placing unit 2c all arranged in the X direction. The substrates W held in a common carrier SC are transferred from the outside of the apparatus to the first carrier placing unit 2b, cleaned in the substrate processing unit 3b, and transferred from the second carrier placing unit 2c to the outside of the apparatus while held in the common carrier SC.