Objective This study aimed to investigate the effects of JiaYanKangTai granules on immune- associated cytokines in rats with autoimmune thyroiditis, and the mechanisms for treating autoimmune thyroiditis. Methods 30 Lewis rats were randomly assigned into the control group (CON, n= 10) and the induced group (n= 20). The induced rats were then randomly divided into the model group (EAT, n= 10) and the administrative group ( JYKT, n= 10) after immunization by subcutaneous injections of thyroglobulin and drinking iodine-containing water for 7 weeks. Rats of the JYKT group were administrated JiaYanKangTai granules for 8 weeks. The expression levels of anti-thyroperoxidase (TPOAb) and anti-thyroglobulin ( TGAb) were detected. Pathological changes of the thyroid were observed. Gene and protein expression levels of multiple cytokines were detected by qPCR and antibody arrays, respectively. Differentially- expressed cytokines were analyzed and cluster heatmapping was performed. Results Expression levels of TPOAb and TGAb were significantly higher in the EAT group than those in the CON group. Pathological changes to the thyroid were alleviated in the JYKT group compared with those in the EAT group. Gene expression levels of chemokine C-C Motif Chemokine Ligand 3 (CCL3), C-X3-C motif chemokine ligand 1 (CX3CL1), interleukin-17 (IL-17), interferon-γ (IFN- γ) and tumor necrosis factor-α (TNF-α) were significantly higher in the EAT group than those in the CON group. Gene expression levels of CCL3, CX3CL1, IL-4, IL-17, IFN-γ and TNF-α were significantly lower in the JYKT group than those in the EAT group. Differential-expressed cytokines were well-clustered. Protein expression levels of CCL3, CX3CL1 and IL- 17 were significantly higher in the EAT group than those in the CON group. Protein expression levels of CCL3, CX3CL1, IL-4, IFN-γ and TNF-α were significantly lower in the JYKT group than those in the EAT group. Conclusions JiaYanKangTai granules alleviated damage of the thyroid in autoimmune thyroiditis by regulating immune-related cytokines.