A channel estimation algorithm is des igned based on intra-symbol frequency-domain averaging (ISFA) method to estima te and equalize the dispersion impairments of polarization division multiplex op tical orthogonal frequency division multiplexing (PDM-O-OFDM) system.The proposed c hannel estimation algorithm is improved from pilot-based intra-symbol frequency-domain averaging algorith m by Kaiser Window function. The improved algorithm can increase accuracy of post channel estimation processi ng,and can improve the bit error rate(BER) and optical signal to noise ratio (OSNR) of long haul PDM-O-OFDM system. The parameters of the algorithm are determined by means of simulation test,and t he equalization performance of long haul dispersion impairments is analyzed.The simulation results show that the propos ed algorithm is better than the original algorithm when propagating distance is longer than 700km,and has a 0.35dB lower OSNR penalty than the original algorithm at 900km.