The complexity of atmospheric channel will cause the random change of channel state parameters, which will have great influence on communication system performance. Thus, the dust optical channel estimation based on training sequence is researched in this paper. Choosing the m sequence as training sequence and adopting time division multiplexing (TDM) technology, an estimation scheme is constructed based on training sequence. Employing the 0 sequence of the training sequence, a noise variance estimation method is constructed in this scheme. On this basis, the impacts of the scattering path number and the training sequence length on the mean square error (MSE) of channel estimation and bit error performance under MMSE criterion are researched. The results show that the number of scattering path should not exceed 5, and 63 is an appropriate choice for m sequence length under MMSE criterion for the low signal to noise ratio atmospheric channel.