Zero point shift based on thermal siphon effect occurring actually when a substrate is processed is detected accurately and corrected suitably. The semiconductor fabrication system comprises a gas supply passage (210) for supplying gas into a heat treatment unit (110), an MFC (240) for comparing an output voltage from a detecting unit for detecting the gas flow rate of the gas supply passage with a set voltage corresponding to a preset flow rate and controlling the gas flow rate of the gas supply passage to the set flow rate, and a control unit (300). The control unit replaces gas in the MFC by gas which is to be used at least for processing a substrate before the substrate is processed, detects the output voltage from the MFC under a state where valves (230, 250) provided in the upstream and the downstream of the MFC are closed and stores the detected output voltage in a storage unit, corrects the set voltage corresponding to the flow rate of gas to be used for processing the substrate based on the output voltage from the MFC stored in the storage unit at the time of processing the substrate, and sets the corrected set voltage in the MFC.