The Fabry-Perot(F-P) etalon was commonly used in direct detection Doppler wind lidar. As a considerable affect would be caused by laser frequency drift in transmittance curve estimation, a new transmission curve fitting algorithm based on spectrum estimation was presented. Firstly, the scan result of F-P etalon was reconstructed into observation matrix. The pseudo-spectrum by MISIC algorithm was conducted. Then spectrum peak was searched and the FSR by linear least squares estimation method was calculated. Secondly, the else parameters by nonlinear least square estimation method was estimated with the estimation above. The performance of the proposed method was analyzed by simulation and verified through the real data, the results show that the proposed algorithm is more stable and accurate under limited amount of data. The relative error is less than 1% when SNR is 10 dB and sample interval is 50 step. This method has lower sweep time, less error and realty utility value.