Objective: Serum anti Müllerian hormone (AMH) was used to evaluate the effect of cyclophosphamide (CTX) on ovarian function in female patients with systemic lupus erythematosus (SLE). Methods: A total of 121 female patients who were 18-50 years old with normal menstruation were selected. Among them, 54 patients were treated with CTX as the study group and the remaining 67 cases as the control group. Before and after treatment for 6 months, the clinical characteristics, menstruation and AMH level of all patients were recorded and detected. At the same time, the method of using CTX and the cumulative measurement are recorded. Results: (1) Before treatment, there was no significant difference in AMH and mean age, duration of disease and SLEDAI score between the CTX treatment group and the control group. The renal injury in the CTX treatment group (44.4%) was higher than that of the control group (34.3%), and the difference was statistically significant (P<0.05). (2) After 6 months of treatment, the AMH of group CTX decreased from (2.39±1.58) μg/L to (1.56±1.42) μg/L, and the difference was statistically significant (P<0.01). But there was no significant change in the control group. In 54 cases of CTX treatment group, 23 cases (42.6%) had different degree of menstrual abnormalities, while 67 cases had only 8 cases (11.9%) in the control group. Moreover, the AMH level of 31 cases with abnormal menstruation was (0.95±0.59) μg/L, which was significantly lower than that of the other 90 normal cases (2.36±1.58) μg/L. (3) In 54 cases of CTX treatment group, the cumulative dose of CTX was less than 3 g in 14 cases, 33 cases of 3-6 g, 7 cases greater than 6 g. AMH was all were lower than those before treatment. But there was a statistical difference between the 3 g group and 3-6 g group before treatment, and there were statistical differences between the groups. Conclusion: CTX can damage ovarian function in women of childbearing age SLE. Low dose intravenous CTX may have less damage. Serum AMH can be used to monitor ovarian function in patients with SLE and to guide individualized treatment.