We present an extra processing added to conventional least square(LS) channel estimation to further improve its performance in coherent optical orthogonal frequency division multiplexing(CO-OFDM) system. The influence of noise, chromatic dispersion and polarization mode dispersion on the performance of the proposed algorithm is analyzed. The simulation results show that the improved algorithm has better performance and lower complexity. We present an extra processing added to conventional least square (LS) channel estimation to further improve its performance in coherent optical orthogonal frequency division multiplexing (CO-OFDM) system. The influence of noise, chromatic dispersion and polarization mode dispersion on the performance of the proposed algorithm is analyzed. The simulation results show that the improved algorithm has better performance and lower complexity.