Disclosed is a mass flow controller system which makes it possible to precisely control an output flow rate by means of a mass flow controller. In the mass flow controller system, data giving information about the relationship between flow rate values of a reference gas and CF values of a sample gas are stored; a target flow rate is converted into a reference gas flow rate using a predetermined CF value; a sample gas flow rate is calculated from the converted reference gas flow rate and the CF value corresponding to the reference gas flow rate; the sample gas flow rate is compared with the target flow rate; and the CF value used for the reference gas flow rate conversion or the sample gas flow rate calculation is updated using the corresponding relationship therebetween.
