In a substrate treatment system, a stocker device, a single-wafer treatment device, an interface device, and a batch treatment device are disposed in a line and linearly in this order. A first transport robot of the stocker device transports a carrier placed on a load port to a stocker device side position. A carrier transport mechanism transports the carrier from the stocker device side position to an interface device side position. A second transport robot of the interface device transports the carrier from the interface device side position to a shelf. The batch treatment device takes out a plurality of substrates from the carrier transported to the shelf, and performs predetermined batch treatment on the plurality of taken-out substrates. The single-wafer treatment device performs treatment on a plurality of substrates one by one.