Mastitis causes serious economic losses in the dairy industry, but there are no effective treatments or preventive measures. In this study, theZRANB3,PIAS1,ACTR3,LPCAT2,MGAT5, andSLC37A2genes in Xinjiang brown cattle, which are associated with mastitis resistance, were identified using a GWAS. Pyrosequencing analysis showed that the promoter methylation levels of theFHITandPIAS1genes in the mastitis group were higher and lower, respectively, than those in the healthy group (65.97 ± 19.82% and 58.00 ± 23.52%). However, the methylation level of thePIAS1gene promoter region in the mastitis group was lower than that in the healthy group (11.48 ± 4.12% and 12.17 ± 4.25%). Meanwhile, the methylation levels of CpG3, CpG5, CpG8, and CpG15 in the promoter region of theFHITandPIAS1genes in the mastitis group were significantly higher than those in the healthy group (p< 0.01), respectively. RT-qPCR showed that the expression levels of theFHITandPIAS1genes were significantly higher in the healthy group than those in the mastitis group (p< 0.01). Correlation analysis showed that the promoter methylation level of theFHITgene was negatively correlated with its expression. Hence, increased methylation in the promoter of theFHITgene reduces the mastitis resistance in Xinjiang brown cattle. Finally, this study provides a reference for the molecular-marker-assisted selection of mastitis resistance in dairy cattle.