Disclosed is a substrate processing system capable of suppressing inflow of dust into the region where semiconductor substrates are placed, when semiconductor substrates are stacked using a pair of substrate holders. The substrate processing system comprises: a substrate holder system in which a first substrate holder that holds a first substrate and a second substrate holder that holds a second substrate are placed facing each other in order to clamp the first substrate and the second substrate therebetween; and a dust inflow prevention section including a processing device that holds the substrate holder system and that prevents inflow of dust into the region where the first substrate and the second substrate are clamped, in the substrate holder system and/or the processing device. The substrate holder system may be provided with a dust inflow prevention mechanism that prevents inflow of dust into the region where the substrates are held, in either of the substrate holders.
