A substrate processing apparatus detects malfunction of mechanisms in MFC. An inert gas supply line, a first shut-off valve shutting off the inert gas supply, a process gas supply line, and a second shut-off valve shutting off the process gas supply are installed upstream of the MFC. A gas supply pipe connected to a process chamber, a third shut-off valve shutting off gas supply to the gas supply pipe, an exhaust vent line which is exhaustible, and a fourth shut-off valve shutting off gas supply to the exhaust vent line are installed downstream of the MFC. A main control unit determines that the MFC is abnormal if a transition time exceeds a previously set time when the MFC transitions from a closed state to an opened state while the shut-off valves are in a closed state.