A method of calibrating a zero point of a mass flow control device includes closing a valve installed in a main flow path of the mass flow control device to block the main flow path and prevent a fluid from flowing in the main flow path, determining, based on a pressure value measured using a pressure meter installed in the main flow path, whether the fluid has stopped flowing, determining, based on a flowrate value measured by a flowrate sensor provided on a sensor flow path connected to the main flow path, whether the fluid is stable, calculating a zero point calibration value based on a temperature value of the fluid measured by a thermometer installed in the main flow path and the flowrate value measured by the flowrate sensor, and applying the zero point calibration value to a zero point of the flowrate sensor.