An atmosphere channel testing link is set up in the marine environment, and the experimental data are tested, including the atmosphere refractive configuration index, the variance of beam drifting and the beam radius. The comparison of free space optics bit error rate (BER) model with none of pointing error and the one with pointing error is carried on. Based on the BER model with pointing error, the BER performance of free space optics system is estimated with the refractive configuration index, beam drifting and beam spreading. Experimental results show that the actual measured BER increases with the atmosphere refractive configuration index. When the atmosphere refractive configuration index is small, the actual measured BER is larger 10 to 20 orders of magnitude than the theoretical calculated BER on account of the effect of beam drifting and beam spreading.