Aiming at the problem that atmospheric turbulence reduces the bit error performance of communication system in free space optical communication, a new decoding method of segmented polarization code cyclic redundancy check serial cancellation list (PC-CRC-SCL) based on relaxed polarization code is proposed. The algorithm is applied to free space optical communication system and simulated under weak atmospheric turbulence intensity. The simulation results show that when the bit error rate is 10-4, compared with the segmented CRC-SCL decoding algorithm of the fully polarized code, the segmented PC-CRC-SCL decoding method based on the relaxed polarizatio code obtains an additional coding gain of 0.3 dB, and the complexity of the polarization code encoding and decoding is reduced by 10% to 20%, and the bit error performance of free space optical communication system is significantly improved.