A substrate treatment system includes: a treatment station including a plurality of treatment apparatuses; an interface station which delivers a substrate to/from an exposure apparatus provided outside the system and including a plurality of exposure stages; a plurality of substrate inspection apparatuses; a substrate transfer mechanism which transfers the substrate between each of the treatment apparatuses in the treatment station and the substrate inspection apparatus; and a control apparatus which identifies an exposure stage which has been used in exposure processing of a substrate from among the plurality of exposure stages, and controls the substrate transfer mechanism to transfer the substrate after the exposure processing to a substrate inspection apparatus previously made to correspond to the identified exposure stage.