Aiming at the problem that there is no suitable construction method of the polarization code for atmospheric turbulence channels at present. Based on the wireless optical communication system, this paper proposes to apply Gaussian partial order to the construction of polar code sequences in atmospheric turbulent channels. The method of constructing polarization codes by Gaussian partial order algorithm is described in this paper. Monte Carlo simulation is used in Matlab to analyze the error rate of 32 sub-channels under σ■■=0.2 turbulent channel and the transmission error probability under different turbulence intensity, and constructed with Gaussian partial order method. The simulation results show that the reliability order of the sub-channels in the weak turbulence channel is basically the same as the polarization code sequence constructed using the Gaussian partial order method, which proves that free space optical communication can use Gaussian partial order method to construct the polarization code sequence in the weak turbulence channel.