To reduce the influence of fiber dispersion,channel noise and phase no ise of laser in coherent optical orthogonal frequency division multiplexing (CO-OFDM) system,we present a new channel estimation method based on analysis of phase noise compen sation (APNC) algorithm.This method relies on LS estimation,and then uses impulse response pro cessed with window (IRW) algorithm to f ilter the noise outside the window and to ensure the length of channel impulse respons e in OFDM guard interval.On the side of the algorithm complexity,IRW method is not more enormous than LS algorithm.The phase noise model of CO-OFDM system is analyzed to compensate the phase noise within the channel impulse response length,and further to improve the accuracy of channel estimation.The simulation results show that if the CO-OFD M system has 256subcarriers,the complex multiplying number of APNC algorithm is improved by only 0.125time than IRW algorithm.And with the same system′s BER,the requirement of SNR in IRW algorithm is nearly 0.5dB lower than that in LS algor ithm.