Objective:To investigate the effect of human interferon-α-2b(IFN-α-2b) in the treatment of endometriosis by detecting the levels of CA125 and endometrial antibody(EMAb). Methods: Forty-five cases with endometriosis were divided into three groups. Fifteen cases in test group (operation+IFN-α-2b), 20 cases in control group A (operation+Diphereline), 10 cases in control group B(only operation). The blood serum level of CA125 was detected by microparticle enzyme immunochemiluminescent at pre-operation, the first month, second month and third month of the post-operation; and the EMAb level was measured by enzyme linked immunosorbent assay (ELISA). The follow-up of patients was carried out after operation to evaluate the clinical appearances and record the adverse effects of the human IFN-α-2b. Results: Compared with pre-operation, the levels of CA125 and EMAb were obviously degraded in the first to third months after surgery in test group and control group A(P < 0.05). There were no significant difference in the levels of CA125 and EMAb were at pre-operation,the first month,second month and third month of the post-operation between the test group and control group A(P > 0.05). There were no significant difference in the levels of CA125 and EMAb at pre-operation between the test group and control group B(P > 0.05). However, the level of EMAb was lower the first month after operation in the test group than that of control group B. In the follow-up, the adverse effects of the human interferon-α-2b were observed including low-grade fever, articular muscle soreness and gastrointestinal tract complaints. These appearances completely disappeared after drug withdrawal. It had less impact on the menstruation. Conclusion: The levels of CA125 and EMAb were similar in treatment of endometriosis with human IFN-α-2b and with Diphereline. Both of the treatments are better than the pure surgery. It has less impact on the menstruation and can avoid menostasia.