Objective To explore the impacts of cSNP on the structure and function of rhesus macaque's BST-2. Methods Extracting RNA from peripheral blood of rhesus macaques, then RT-PCR, Monoclonal sequencing to find the cSNP sites; Forecasting the structure of these proteins; Comparing the Level of SIVmac239 replication between the different genotypic Rhesus macaques. Results We found 8 non-synonymous mutation sites, in the 8 non-synonymous mutation sites, Only G41A, T128C, C129 and A333C change the secondary protein structure of BST-2 by forecasting of Psipred software; At the plateau of SHIVSF162p3 replication, The SHIVSF162p3 replication level of reference genotype rhesus macaque (DLQ) is higher than rhesus macaques of GLQ genotype, other genotypes rhesus macaques have no significant difference. Conclusion cSNP (G41A) may influence the antiviral activity of rhesus macaque's BST-2, this study gives us a reference to further research work.