Aiming at the problems of high computational complexity of traditional discrete Fourier transform(DFT) channel estimation algorithm and inefficient channel coefficients in cyclic prefix(CP) in direct-current biased optical orthogonal frequency division multiplexing system, an improved channel estimation algorithm based on Hermite symmetric DFT(H-DFT) threshold is proposed. Firstly, according to the property that the time domain response of the channel is transformed to the frequency domain to satisfy the Hermite symmetry, the frequency domain response of all the subcarriers can be obtained by only making Hermite symmetry for the frequency domain response of the effective subcarriers. Secondly, according to the average power of the noise outside the CP, the threshold value is set for the channel tap data inside the CP to filter the noise inside the CP. Compared with the traditional DFT channel estimation algorithm, the simulation results show that the H-DFT threshold improved channel estimation algorithm can effectively reduce the computational complexity, and improve the bit error rate and mean square error.