Objective: To study the effect of Neiyi-Tongjingling on the content of TGF-β1 and Smad2/3 protein in ectopic endometrium of rats with endometriosis. Methods: Atotal of 42 rats were randomly divided into the sham operation group, model group, high, medium and low dose groups of traditional Chinese medicine and western medicine group with 7 rats in each group. Except for the sham-operated group, the rats in the other groups established EMs models by means of rat autologous intimal transplantation. The drug was administered at the 5th week after the model was established. The western medicine group was given 0.5 mg/kg gestrinone solution twice a week. The high, medium and low dose groups of traditional Chinese medicine were given 49.50 mg/kg, 24.75 mg/kg and 12.38 mg/kg of Neiyi-Tongjingling liquid, respectively. While the model group and sham operation group were given the same volume of normal saline once per day for 4 weeks. The volume of ectopic lesions in each group was observed. The HE staining was used to observe the pathological changes of intima tissue. Immunohistochemical SP method was used to detect the expression of TGF-β1 and Smad2/3 proteins in intima tissue. Results: The volume of ectopic endometrium (57.91 ± 13.10 mm³, 48.93 ± 8.15 mm³, 76.21 ± 17.14 mm³, 57.88 ± 15.98 mm³ vs. 141.58 ± 54.25 mm³) in the western medicine group and the high, medium and low dose group of Chinese medicine were significantly lower than that in the model group (P<0.05). Compared with the model group, the content of TGF-β1 (0.08 ± 0.00, 0.08 ± 0.01, 0.10 ± 0.00 vs. 0.13 ± 0.03) and Smad2/3 (0.09 ± 0.02, 0.08 ± 0.01, 0.10 ± 0.01 vs. 0.12 ± 0.02) in ectopic endometrium tissue of three Chinese medicine groups decreased significantly (P<0.05). Conclusions The Neiyi-Tongjingling can treat EMs by inhibiting the growth of ectopic endometrium, reducing the volume of ectopic lesions, and reducing the expression of TGF-β1 and Smad2/3 proteins.