Objective: To investigate the impact of laparoscopy assisted methotrexate (MTX) sclerotherapy and laparoscopic cystectomy on the ovarian reserve based on serum anti-Mullerian hormone (AMH) level in ovarian endometrioma patients Methods: From June 2016 to June 2020, 18 patients with ovarian endometrioma underwent laparoscopic cyst aspiration followed by in situ methotrexate injection (Group 1: surgery + MTX sclerotherapy) and 180 patients underwent laparoscopic cystectomy (Group 2: surgery). Using analysis of covariance (ANCOVA), comparing the rate of decline of the serum AMH level between the two groups adjusted for the five covariates (preoperative AMH, age, BMI, Total O SIZE (sum of both ovaries size), cyst laterality) was done. Subgroup analyses controlled for age, Total O SIZE and cyst laterality were done. Results: There is no significant difference in the rate of decline of the serum AMH level between the Group 1 and Group 2 adjusted for the covariates (P =0.7366.). But the postoperative reduction of AMH level was comparatively less in Group 1 than Group 2 (Lsmean -33.1151. VS. -38.4669. ). In all the subgroup analysis, there is no significant difference in the percentage change of AMH between Group1 and Group2. But in the bilateral endometrioma group and the below 30 years old group analysis, decline of AMH level was relatively less in MTX sclerotherapy group. Conclusion: Compared with conventional surgical treatment of ovarian endometrioma having a negatively impact on post-operative ovarian reserve, MTX sclerotherapy showed non-inferiority. Especially the patient of bilateral ovarian endometrioma or age below 30 may expect a more favorable outcome in terms of decreased ovarian reserve. For ovarian endometrioma patient who want to get pregnant, MTX sclerotherapy could be better option.