In order to improve the phase difference measurement accuracy and reduce the computational complexity of the ApFFT algorithm, improved ApFFT algorithm is proposed. The improved algorithm is based on the data processing process of the ApFFT algorithm, reducing the number of overlapping data between segments from N-1 to N-m, forming the largest integer with a new number of segments not greater than (N-1)/m+1, through FFT operation, the accurate phase can be measured from the peak spectra of the spectrum. Through experimental analysis, it is verified that the phase estimation RMSE of the improved ApFFT algorithm is between the ApFFT algorithm and the CRLB of two-parameter, in application, which can improve the measurement accuracy of the ultrasonic flow meter.