A substrate processing system includes a chamber group including chambers configured to process a substrate in a desired process gas, a gas box group including gas boxes configured to supply the process gas to each of the chambers, a flow rate measuring device configured to measure a flow rate of the process gas supplied from the gas box group, and an exhaust device connected to the chamber group and the flow rate measuring device. The flow rate measuring device includes a measuring instrument and a measurement pipe connected to the gas box group and the measuring instrument and configured to flow the process gas through the gas box group and the measuring instrument. The measurement pipe includes branch pipes connected to each of the gas boxes, a main pipe connected to each of the branch pipes and the measuring instrument, and branch pipe valves provided in the branch pipes.