Transcriptomics was used to analyze the protective effect of diosgenin on autoimmune thyroiditis (AIT) in rats and its possible mechanism. Forty AIT model rats were established following high iodine induction and injection of porcine thyroglobulin adjuvant into Lewis rats. AIT-model rats were treated with an oral gavage(diosgenin) for 8 weeks. The concentrations of T3, T4, FT3, FT4, TSH, TRAb, TPOAb and TgAb in rat serum were detected. The unilateral thyroid lobes of rats were detected by transcriptomes, RT-qPCR (S100A9, PKA, Creb, Epac, and Rap1 mRNA), and Immunohistochemistry (cAMP, PKA, and Creb). The results showed that the expression of serum T3, T4, FT3, FT4, TSH, TgAb, and TPOAb in the high-dose group was greater than that in the low and middle-dose groups. And compared with the AIT-model group, the relative expression of cAMP, PKA and Creb mRNA and protein increased, S100A9 mRNA decreased in the diosgenin groups. To sum up, diosgenin can improve the expression of T3, T4, FT3, FT4, and TSH in AIT model rats, and decrease the concentrations of TRAb, TgAb and TPOAb, which may be related to activation of the cAMP/PKA/Creb pathway and downregulating the expression of S100A9 gene.