A joint method of coherent optical orthogonal frequency division multiplexing (CO-OFDM) channel estimation based on wavelet denoising and improved intra-symbol frequency domain average (ISFA) is proposed. This method can be divided into three steps. Firstly, channel estimation is performed by least square (LS) method; secondly, the wavelet denoising processing is made for the results of estimation; finally, ISFA algorithm improved by Kaiser- window function is applied to the wavelet processing results. The simulation results show that the proposed method can effectively improve the precision of channel estimation. When the optical signal-tonoise ratio (OSNR) is 17 dB, bit error rate (BER) performance of the proposed method can be improved nearly one order of magnitude than that of ISFA method.