There is provided a substrate processing system including an etching apparatus configured to supply a gas containing fluorocarbon to generate plasma so as to perform an etching process on a film including silicon formed on a substrate, wherein the etching process is performed by using plasma through a mask formed on the film including silicon, a film forming apparatus configured to supply a gas containing carbon so as to form a film including carbon on the etched film including silicon. The film forming apparatus is provided separately from the etching apparatus, the etching apparatus performing, a first etching step in which the film including silicon is partway etched by using plasma; and a second etching step in which the film including silicon, on which the film including carbon is formed, is further etched by using plasma, the film forming apparatus performing a film forming step in which the film including carbon is formed, without generating plasma, on the film including silicon on which the first etching step has been performed.