Objective To investigate the influence of GnRH-α medication before minimally-invasive operation on the levels of sex hormone, antral follicle count (AFC) and peak systolic velocity (PSV) of matrix blood flow in the patients with ovarian endometriotic cysts. Methods Totally 140 patients with ovarian endometriotic cysts were chosen and randomly divided into control group (70 patients) with minimally-invasive endoscopy used alone and intervention group (70 patients) with GnRH-α before operation. The operation time, intraoperative blood loss, postoperative body temperature, postoperative intraperitoneal drainage volume, postoperative exhaust time, the levels of sex hormone, anti-Mullerian tube hormone (AMH), AFC and PSV of both groups were compared. Results Using t test to compare the two groups, the levels of perioperative clinical indicators in the intervention group were better than those of the control group, the operation time and exhaust time were shorter, the intraoperative bleeding volume and postoperative abdominal drainage volume were smaller, and postoperative temperature was lower in the intervention group than in the control group with significant differences (P < 0.05). There was no statistical difference in any index between the two groups before treatment (P > 0.05). Compared with the levels before treatment, follicle-stimulating hormone (FSH) level statistically increased, and estradiol and AMH levels significantly decreased 6 months after operation in both groups (P < 0.05). The levels of FSH, AFC and PSV in the intervention group were higher than those in the control group, but the AMH expression was lower than that of the control group 6 months after operation (P < 0.05). There was no significant difference in estradiol level between the two groups 6 months after operation (P > 0.05). Conclusions GnRH-α premedication in the treatment of patients with ovarian endometriotic cysts by minimally-invasive operation can efficiently shorten the operation time, reduce the degree of surgical trauma, speed up the recovery process after operation and improve the level of sex hormone, and is helpful to improve the ovarian reserve function.