There is provided a substrate processing apparatus of performing a predetermined substrate process on a plurality of target substrates under a vacuum atmosphere, including: a plurality of processing parts each configured to perform the substrate process on each of the plurality of target substrates; a gas supply mechanism configured to supply a processing gas to each of the plurality of processing parts; a single exhaust mechanism configured to exhaust the processing gas within the plurality of processing parts; and a control part configured to control the single exhaust mechanism to collectively exhaust the processing gas within the plurality of processing parts, and control the gas supply mechanism to separately supply the processing gas into each of the plurality of processing parts such that a difference between internal pressures of the plurality of processing parts is prevented.