Abstract: A substrate processing system is disclosed, comprising: a vacuum transfer module; a substrate processing module connected to the vacuum transfer module and configured to process a substrate in a depressurized environment; a load-lock module connected to the vacuum transfer module; at least one substrate cooling stage disposed in the load-lock module; at least one substrate transfer robot disposed the vacuum transfer module and having at least one end effector; and a controller configured to control a particle removal operation. The operation includes: cooling at least one dummy substrate placed on said at least one substrate cooling stage to a first temperature; and holding said at least one end effector in any one of a plurality of positions in the vacuum transfer module or the substrate processing module for a first time period in a state where at least one cooled dummy substrate is placed on said at least one end effector.