Objective To compare the clinical efficacy between the vaginal ovarian cystectomy and the laparoscopic ovarian cystectomy. Methods A total of 104 patients with ovarian cyst hospitalized in our hospital during June 2013-June 2016 were selected and divided into observation group (vaginal ovarian cystectomy, n=55) and control group (laparoscopic ovarian cystectomy, n=49). There were no significant differences in mean age, body mass index (BMI), abdominal surgical history, cyst diameter and cyst type between the two groups. The operation time, blood loss in operation, hospitalization expenses and average hospital stay were observed in the two groups. The ovarian reserve function before and after the operation was also observed. Results The operation time [(46.9±18.4 min)], hospitalization cost [(8165.3±951.8) yuan] and the average length of hospital stay (4.5 ± 1.9 days) were significantly less in the observation group than those of the control group [(62.3 ± 26.5) min], [(12543.9 ± 1464.4) yuan] and [(6.8 ± 2.3) days], (P<0.05). Before the operation, there were no significant differences in estradiol (E2), follicle stimulating hormone (FSH)/luteinizing (LH), FSH and antral follicle count (AFC) between the two groups. After the operation, the values of FSH/LH (1.4±0.4 vs. 1.8±0.6) and FSH [(9.2±2.9) U/L vs. (13.6±4.3) U/L] were significantly decreased in the observation group than those of the control group. The AFC (7.2±1.6 vs. 6.0±1.3) was significantly more in the observation group than that of the control group (P<0.05). Conclusion The vaginal ovarian cystectomy is of little damage to ovarian reserve function, which is suitable for women of child-bearing age and conforms to the requirement of"value medicine".