The Mass Flow Controller(MFC) has become crucial in semiconductor manufacturing equipments. It is an important element because the quality and the yield of a semiconductor process are decided by the accurate flow control of gas. Therefore, the demand for implementing the high speed and the highly accurate control of MFCs has been increasing. It is hard to find an article of the control algorithm applied to MFCs. But, it is known that commercially available MFCs adopt PID control algorithms. Particularly, when the system detects the flow by way of heat transfer, the MFC control problem includes the slow response and the nonlinearity. In this paper, MFC control algorithm with a superior performance to the conventional PID algorithm is discussed and the superiority is demonstrated through the experiment. A fuzzy controller was utilized in order to compensate the nonlinearity and the slow response, and the performance is compared with that of an MFC currently available in the market. The control system, in this paper, consists of a personal computer, the data acquisition board and the control algorithm carried out by LabWindows/CVI program on the PC. In addition, a method of estimating the actual flow from the sensor output with the slow response is presented. In conclusion, according to the result of the experiment, the proposed algorithm shows better accuracy and is faster than the conventional controller.