A mass flow controller with high accuracy flow rate output control is disclosed. In the mass flow controller, relation data that indicates a corresponding relation between a flow rate of a reference gas and a CF value of a sample gas is stored, a target flow rate is converted into a reference gas flow rate by the use of a predetermined CF value, a sample gas flow rate is calculated from the converted reference gas flow rate and a 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 that is used for conversion of the reference gas flow rate or calculation of the sample gas flow rate is updated by the use of the corresponding relation based on the error between the sample gas flow rate and the target flow rate.