Abstract: Autoimmune thyroid disease（AITD） is an organ-specific autoimmune disease mainly mediated by T cells, including Graves disease（GD） and Hashimoto thyroiditis（HT）. The incidence of AITD is closely related to genetic factors. The aim of this study is identifying susceptibility genes and loci associated with AITD. In this study, the genomes of 100 patients with AITD（51 HT and 49 GD） and 50 healthy subjects were sequenced in targeted regions, and the correlation between gene polymorphisms and AITD was statistically analyzed, and further linkage analysis was performed to find susceptibility genes and associated loci in genes. In this study, five SNP loci（rs12205059, rs62408219, rs7742121, rs7756574, rs12204886） in BACH2 gene were found to be completely linked, ten SNP loci（rs12778514, rs3740354, rs3740353, rs9633555, rs9633557, rs9633534, rs3740352, rs2393730, rs2393729, rs2393728） in ARID5B gene were highly linked, seven SNP loci（rs230528, rs230526, rs230521, rs230517, rs230512, rs4648011, rs230505） in NFKB1 gene were highly linked, and they showed significant correlation with GD; twenty-four SNP loci（rs77175037, rs16882370, rs77758469, rs78777913, rs117721419, rs78336372, rs76671310, rs76587383, rs75249386, rs79815784, rs57765055, rs75199762, rs75340880, rs9444735, rs61246723, rs9451336, rs78318422, rs117023048, rs74639869, rs75487886, rs80029445, rs78252829, rs60148132, rs58745003） in BACH2 gene were completely linked, and four SNP loci（rs60519986, rs56835438, rs58205153, rs9451298） were highly linked, showing significant correlation with HT; four SNP loci（rs12205059, rs7742121, rs7756574, rs12204886） in BACH2 gene were highly linked, and five SNP loci（rs9633555, rs9633556, rs2393730, rs2393729, rs2393728） in ARID5B gene were highly linked, and they all showed significant association with GD and HT susceptibility. This study reveals that the polymorphisms of BACH2, ARID5B and NFKB1 genes are associated with AITD susceptibility, and they may be involved in the pathogenesis of AITD.