The short time Fourier transform (STFT) and continuous wavelet transform (CWT) cannot resolve slowly varying velocity at low velocity stage in most photonic Doppler velocimetry (PDV) data. A new analysis method based on Fourier transform is presented to overcome this shortcoming. Instead of extracting the frequency of interference signal for velocity analysis, the new method uses a modified Fourier transform to analysis the phase of signal, and converts phase to displacement or velocity. The validity of the proposed method is examined in experimental data of a plate- impact experiment, which distinguishes the elastic- plastic properties of Fe sample. The method not only uses all sampling points of the raw data, but also has a higher velocity resolutions especially for low velocity stage. The method is a supplement to STFT and CWT method.