Atmospheric turbulence will lead to the deterioration of the atmospheric laser communication link bit error rate performance. A frequency domain deconvolution method restrained multiplicative noise is proposed in the atmospheric laser communication system. The method is effective to connect the atmospheric laser communication with deconvolution technology. Fast Fourier transform (FFT) module is added to the algorithm, converting the signal into frequency-domain, deconvolution filtering in the frequency-domain, reduces the algorithm complexity. Using atmospheric laser communication measurement system on a rainy day to experimental verification algorithm, contrast before and after deconvolution signal modulation constellation diagram and analyze the system bit error rate. The experimental results show that the frequency-domain deconvolution can reduce the bit error rate of atmospheric laser communication system and is a kind of effective method of multiplicative noise inhibition of atmospheric channel.