Porcine reproductive and respiratory syndrome virus (PRRSV) could infect porcine alveolar macrophages (PAM), and the CD169 and CD163 are identified as critical receptors on the surface of PAM, but whether the single nucleotide polymorphisms (SNPs) of these genes could influence the infection is remain unclear. In this study, we identified totally 6 SNPs for CD169 (G1640T, C1654A, C4175T) and CD163 (G2277A, A2552G and C2700A), and evaluated their associations with PRRSV infection using two classified methods in a 524 pig population to investigate the effects of mutations on the PRRSV receptors. The pigs with genotypes of AA of CD169-C1654A, CT of CD169-C4175T and AA of CD163-A2552G appeared to resistant to the PRRSV infection by the combination of two classified results. The results provided fundamental molecular investigation to promote pig breeding with disease resistance. However, the identification of functional changes induced by SNPs and molecular mechanism were need further research.