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OBJECTIVE: To observe the effect of herb-partitioned moxibustion（HPM） on the miRNA expression profile of thyroid tissue in experimental autoimmune thyroiditis（EAT） rats.METHODS: Rats were randomly divided into normal control（NC） group, EAT model（EAT） group,HPM group and western medicine（Med） group.EAT model rats were prepared by a combined immunization with complete and incomplete Freund’s adjuvant emulsified with porcine thyroglobulin and iodine. Rats in the HPM group were treated with HPM, while rats in the Med group were treated with levothyrocine（1 μg/2 m L） by gavage. HE staining was used to observe the pathological morphological changes of thyroid tissue,ELISAs was uaed to detect the serum concentrations of TGAb, TPOAb, FT3, FT4, TSH. We then performed high-throughput mi RNA sequencing to analyse the mi RNA expression profiles in the thyroid tissues, followed by a bioinformatics analysis.RT-q PCR was used to verify the identified differentially expressed mi RNAs.RESULTS: HPM improved the thyroid tissue morphology and reduced serum TPOAb, TGAb, TSH concentration in EAT rats（P < 0.05）, but with no obvious effect on FT3 and FT4 concentration. While the TSH, FT3 and FT4 concentration was significantly changed in the Med group（P < 0.01 or P < 0.05）compared with that of EAT group. Sequencing results showed that a total of 17 mi RNAs were upregulated, and 4 were downregulated in the EAT rats,in which the expression levels of mi R-346 and mi R-331-5 p were reversed by HPM. The target genes of the mi RNAs that regulated by HPM wereassociated with a variety of immune factors and immune signals. RT-q PCR verification showed that the expression of mi RNA-346 and mi RNA-331-5 p was consistent with the sequencing results.CONCLUSIONS: HPM could regulate the the expression of mi RNA-346 and mi RNA-331-5 p, then act on their target genes to immune and inflammation-related pathways, which may be one of the mechanisms of HPM on EAT rats.