A method for signal processing of CMF based on DTFT algorithm with overlap Hanning windows is proposed. First, a new IIR adaptive notch filter is applied to filter the sensor output signals of CMF and calculate the frequency. Then the DTFT algorithm with overlap Hanning windows is introduced to calculate the real-time phase difference between two enhanced signals. With the frequency and phase difference obtained, the time interval between the two signals is calculated and then the mass flowrate is derived ultimately. The simulations and field test results show that the proposed method is efficient.