An algorithm of demodulating dynamic phase difference based on Hilbert transform is proposed according to the principle and signal expression of fiber interference turbulence measurement system. The results of numerical simulation show that waveform phase difference and turbulence′s random phase difference can be demodulated by this method and absolute error is less than 10-3, which is in accordance with the results of correlation method. Compared to the correlated algorithm, the algorithm of Hilbert transform doesn′t have smooth effect on signal and doesn′t need to set correlation length, so it can reflect characteristic of signal frequency better. This research provides a new method for measuring turbulence random phase difference.