After the drying, the cleaning carrier transport robot 31a receives the cleaning carrier WC from the drying part 33, and transports it to the cleaning carrier transfer part 28 of the second carrier placing unit 2c. Then, the substrates held in the cleaning carrier WC are transferred to a common carrier SC placed on the common carrier part 22 of the second carrier placing unit 2c in reverse order to the operation of the first carrier placing unit 2b, and transferred to the outside of the apparatus 1b. Namely, in the substrate processing apparatus 1c, the first carrier placing unit 2b transfers the substrates W only from the common carrier placing part 22 to the substrate processing unit 3b, while the second carrier placing unit 2c transfers the substrates W only from the substrate processing unit 3b to the common carrier placing unit 22.