Background: Endometriosis is a common gynecological disease, which can seriously affect the physical and mental health of patients. However, there is not a satisfactory way to treat endometriosis with a low recurrence rate. Materials and Methods: Including twenty patients with endometriosis given conservative surgery, a prospective clinical study was performed with randomly grouping and positive control. The traditional Chinese medicine (TCM) and western medicine (WM) groups were given Danchi decoction and GnRH-a or gestrinone respectively. Treatment was given in 1-5 days during the first menstruation. The eutopic endometriums were collected before and 3 months after the treatment, respectively. Then immunohistochemistry was performed to obtain the expressions of P450arom and survivin. In the normal control (NC) group no drugs were administered. Results: Before the treatment, the expressions of P450arom and survivin in both TCM and WM groups were much higher than the NC group (P < 0.05) and no significant differences between the two groups (P > 0.05). The expressions of the two groups were remarkably decreased after the treatment (P < 0.05) and they had no difference between the two groups (P > 0.05). Conclusion: Danchi decoction can control the recurrence of endometriosis by restraining abnormal secretion of aromatizing enzyme and regulating cell apoptosis in eutopic endometrium. Excessive expressions of aromatizing enzyme and decreased apoptosis are a possible mechanism of endometriosis recurrence.