Doppler difference interference spectrometer is a kind of Fourier transform spectrometer. In the process of atmospheric wind velocity retrieval, even-prolongated recovered spectrum cannot work out the phase information of the target spectral line directly. Meanwhile, there are stray spectral lines and noises in the recovered spectrum, which make the phase of the interferogram changed and the retrieved wind velocity deviated. Therefore, isolation of the target spectral line is necessary in the process of getting the phase information of the recovered spectrum in actual noisy environment. For interferograms with different signal noise ratios the retrieved wind velocities (SNR) optimized by different window functions with different line widths are analyzed by Monte-Carlo method. The results indicate that the Gaussian window function with line width equaling 4 to 5 times of the spectral resolution provides the best performance if the SNR of the measured interferogram is higher than 26.5 dB, and rectangular window function with line width equaling 7 to 12 times-of the spectral resolution provides the best performance if the SNR of the measured interferogram is lower than 26.5 dB. The phase information and the approximative atmospheric wind velocity can be retrieved.