The characteristics of laser Doppler echo signal are analyzed and a frequency estimation algorithm of laser Doppler signal is presented. The auto-correlation function of signal is obtained by Fast Fourier Transform (FFT) and coarse estimating frequency is acquired from the power spectrum, and then the auto-correlation function is shifted in frequency domain with coarse estimating frequency. The frequency offset is obtained by computing the phase of frequency-shifted signal’s auto-correlation function at one point. The frequency estimation value is acquired by the correction of coarse frequency with frequency offset. The results gotten above and the symmetry of FFT gene can be used to decrease computation complexity. Simulation demonstrates that the method has lower Root Mean Square Error (RMSE) and Mean Absolute Error (MAE). Applied to laser Doppler velocimetry experiment, the result is accordance with simulation.