A method of controlling contamination in a substrate transfer chamber that is disposed between a load port for supporting a container to receive a plurality of substrates and a substrate process module for processing the substrates includes supplying a purge gas into the substrate transfer chamber to purge an interior of the substrate transfer chamber, circulating the purge gas supplied into the substrate transfer chamber through a gas circular pipe, removing particles and airborne molecular contaminants from the purge gas being circulated, and resupplying the circulated purge gas into the substrate transfer chamber.