A gas supply system includes a manifold for supplying gases for processing the substrate to a process chamber; a cleaning gas supply line supplying a cleaning gas to the manifold; a first inert gas supply line supplying a first inert gas to the cleaning gas supply line; a first opening/closing valve opening and closing the cleaning gas supply line; a reaction gas supply line supplying a reaction gas to the manifold; a source gas supply line provided with a vaporizer and supplying the source gas to the manifold; a second inert gas supply line supplying a second inert gas to the manifold and branching out to a carrier gas supply line connected to the vaporizer and a curtain gas supply line bypassing the vaporizer; a second opening/closing valve selectively opening or closing the carrier gas supply line and the curtain gas supply line; and a controller.