Objective To investigate the mechanism of Bupi Qiangli compound in regulating immune system balance in experimental autoimmune myasthenia gravis (EAMG) rats based on the hypothalamic-pituitary-thyroid-thymus (HPTT) axis. Methods A total of 120 Lewis rats were randomly divided into the control group, the model group, the Bupi Qiangli compound groups (low-dose, medium-dose and high-dose groups, 4.75, 7.12 and 9.49 g/kg) and western medicine group (prednisone, 5.4 mg/kg), with 20 rats in each group. Behavioral changes (body weight, Lennon score) were observed during the experiment. After the experiment, histopathological changes of thymus were assessed by HE staining. The serum contents of acetylcholine receptor antibody (AchR-Ab), tumor necrosis factor-β (TNF-β), interleukin-4 (IL-4) and IL-10 were determined by enzyme-linked immunosorbent assay (ELISA). Flow cytometry was used to detect the expression of CD4+CD25+Foxp3+Treg cells in rat thymus. At the same time, HPTT axis function damage index [triiodothyronine (T3), thyroxine (T4), TSH, thyroid stimulating hormone (TSH), thyroid stimulating hormone releasing hormone (TRH), hypothalamic T3 receptor (T3R) and norepineadrenalin (NE)] levels were detected. Results After modeling, compared with the control group, the body quality of each modeling group decreased and the Lennon score increased. After administration, body weights were increased in the Bupi Qiangli compound low-dose, medium-dose and high-dose groups and western medicine group than those of the model group, while values of Lennon score were decreased (P<0.05). HE staining showed degeneration and necrosis of lymphocytes in cortical area, disappearance of thymic bodies in medullary area, and decreased cell number in the model group. The number of cells in thymus cortical area and medulla area of rats were significantly increased in the low, medium and high dose groups of Bupi Qiangli compound and western medicine groups. Compared with the control group, the proportion of CD4+CD25+ Treg and CD4+CD25+Foxp3+ Treg in thymus were decreased in the model group, and the proportion of CD4+CD25-Foxp3+ Treg and CD4+CD25+Foxp3+ Treg were increased (P<0.05). The serum levels of AchR-Ab, TNF-β, IL-4, IL-10, TSH and TRH were significantly increased, while the levels of T3R and NE were significantly decreased (P<0.05). Compared with the model group, the proportion of CD4+CD25+ Treg and CD4+CD25+Foxp3+ Treg were significantly increased in the Bupi Qiangli compound medium-dose and high-dose groups and western medicine group, while the proportion of CD4+CD25-Foxp3+ Treg and CD4+CD25+Foxp3+ Treg decreased. Serum AchR-Ab, TNF-β, IL-4, IL-10, TSH and TRH levels were significantly decreased (P<0.05). T3R and NE levels were increased. Conclusion Bupi Qiangli compound can improve the autoimmune balance of EAMG rats by regulating HPTT axis and related factors.