Abstract: All factors affecting the system error were comprehensive taken into account for Rayleigh Doppler wind lidar in this paper. The calibration accuracy of the transmission curve parameters of the three-channel Fabry-Perot etalon contributes mostly effect to the system error, and the tracking accuracy of laser frequency, aerosol and the estimation error of atmosphere temperature contributing to the system error must be taken into account simultaneously. Experiment results demonstrate that the system error calculated by the calibration parameters error is 10 times bigger than it calculated by the design parameters when the atmosphere temperature and the backscattering ratio are unchanged. The system error increases with the estimation error of atmosphere temperature and the Doppler frequency when the backscattering ratio is constant. The system error produced by the calculation accuracy of the transmission parameters increase with the altitude and the Doppler shift with local maximum value 1.4 m/s at 18 km altitude.