Using the estimation uncertainty of the radial velocity and the detection probability as the evaluation index, the Doppler frequency estimation performance of Periodogram Maximum Likelihood (PML) algorithm was studied. Based on the stratified atmosphere laser echo model, the echo signal was processed by PML and Periodogram Maximum method (PM) respectively to verify the feasibility of PML algorithm. The uncertainties of estimated wind speed and detection probability were analyzed comparatively under the different signal-to-noise ratios condition with PML algorithm. The simulation results show that, with a transmitting pulse width of 400ns and the sampling points of 128, the PML algorithm is suitable for moderate signal-to-noise ratio, and the overall uncertainty of the estimated wind speed is lesser than PM algorithm. When the signal-to-noise ratio is -13 dB, the radial velocity estimation uncertainty is 0.75 m/s and detection probability is more than 90%. This study provides guidance for subsequent field trials.