A method for calibrating a mass flow controller comprising a calibrating valve disposed on the most upstream side of a path, a mass flow rate control valve mechanism, a tank provided at the path on the upstream side of the mass flow rate control valve mechanism, a mass-flow-rate-sensing means, a pressure-sensing means, a means for controlling the mass flow rate control valve mechanism, and a mass flow rate calibration control means, the method comprising the steps of (1) permitting a fluid at a set mass flow rate to flow through the path, (2) setting the mass flow rate control valve mechanism at a degree of opening that the mass flow rate of the fluid is equal to the set mass flow rate, (3) closing the calibrating valve, (4) measuring the pressure and mass flow rate of the fluid after a fluid flow from the tank is stabilized, (5) determining a variation ratio of the pressure and mass flow rate to reference pressure and mass flow rate measured by the same procedures in an initial state, and (6) performing calibration depending on the variation ratio.