Objective To investigate the impact of different kinds of laparoscopic surgery including conventional blunt elimination and modified acute elimination on sex hormone, antral follicle count and ovarian volume of patients with endometriosis (EMs). Methods 100 patients with EMs were chosen from January 2013 to April 2016 and randomly divided into control group (50 patients) with conventional blunt elimination and observation group (50 patients) with modified acute elimination; and the thickness of elimination lesion, the removal rate of ovary cortex, the thickness of ovarian cortex, the level of serum sex hormones, the AFC number of affected side and the volume of ovary before and after operation of the two groups were compared. Results There was no significant difference in the thickness of lesion elimination, the removal rate and removed thickness of ovarian cortical between the two groups (P > 0.05). The thickness of lesion elimination and the thickness of ovarian cortex in middle position of observation group were significantly lower than that in control group (P < 0.05). The thickness of lesion elimination, removed thickness of ovarian cortical and the removal rate of ovary cortex in hilus ovarii in observation group were significantly lower than that in control group (P < 0.05). There was no significant difference in the levels of serum sex hormones before and after treatment between the two groups (P > 0.05). There was no significant difference in the levels of AFC number of affected side before and after treatment (P > 0.05). The levels of AFC number of affected side in hilus ovarii of control group after treatment were significantly lower than that before treatment (P < 0.05). The volume of ovary of both groups after treatment were significantly lower than that before treatment (P < 0.05). The volume of ovary of observation group after treatment were significantly higher than that in control group (P < 0.05). Conclusion Compared with conventional blunt elimination, modified acute elimination in the treatment of patients with EMs can efficiently shorten the operation time, reduce the surgical trauma degree, speed up the recovery process after operation, regulate the level of FSH and AMH and be helpful to protect the ovarian reserve function.