A technique that improves a quality of substrate processing. A substrate processing apparatus includes: a plurality of processing chambers and transfer chambers; a vacuum transfer chamber; a plurality of gate valves; a plurality of first gas supply units to supply an inert gas to a substrate; a transfer robot; and a control unit to control the plurality of first gas supply units and the transfer robot to: supply the inert gas to the substrate at a first flow rate when a distance between a gas supply port and the substrate passing through the plurality of gate valves is a first distance; and supply the inert gas to the substrate at a second flow rate greater than the first flow rate when the distance between the gas supply port and the substrate is a second distance greater than the first distance when the substrate passes through the plurality of gate valves.