In view of the problems that the sampling nonlinearity and the low accuracy of the Fourier transform, a frequency estimation based on phase difference method to measure the distance of the target point is used based on the ranging system of frequency modulated continuous wave, which is based on the equispaced-phase resampling. The principle is analyzed and deduced. The stability of distance measurement and the error of distance measurement are analyzed based on the system. The research results show that the residual error of the measured distance with phase difference frequency measurement and the theoretical distance is not more than 100 μm and the stability of the single point range is between 50-95 μm in the range of 8.3-9.3 m. Compared with the fast Fourier transform, phase difference frequency measurement has better accuracy and stability in ranging.