Purpose To determine the role of vaginal microbiota in the efficacy of cervical cerclage in obstetric outcomes of twin pregnancies. Methods This retrospective study enrolled 68 twin pregnant women diagnosed with cervical incompetence (CIC) and 68 twin pregnancies without CIC. The CIC group was further divided into two subgroups: cerclage group (n = 51) and non-cerclage group (n = 17), according to whether cervical cerclage was performed in the second trimester. Data of vaginal microbiota and obstetric outcomes were collected and compared. Results Cervical incompetence had harmful effect on both pregnancy outcomes and vaginal microecology, characterized by earlier gestational week at delivery (30.3 +/- 5.6 vs 35.6 +/- 1.1, P < 0.001), a lower birth weight of newborns (OR 0.40; 95% CI 0.22-0.74), a higher vaginal pH value (OR 0.11; 95% CI 0.04-0.30) and a lower abundance of Lactobacillus (OR 0.34; 95% CI 0.17-0.70). In addition, compared with the vaginal microbiota after cerclage, less normal diversity of bacterial flora (OR 0.35; 95% CI 0.12-1.01), less Lactobacillus (OR 0.40; 95% CI 0.18-0.91) and more Gardnerellavaginalis (OR 18.92; 95% CI 2.38-150.35) appeared before cerclage. Besides, the unhealthy vaginal environment also had an unfavorable influence on the neonatal outcomes, increased neonatal mortality rate was observed in the group of vaginal pH > 4.5 (P < 0.05). Fortunately, compared with the non-cerclage group, the cerclage group had a longer interval from diagnosis to delivery (>= 8 weeks) and more of the newborns' birth weight were not less than 1500 g (P < 0.05). Conclusion A healthy vaginal environment is essential to improve the obstetric outcome for twin pregnancies with cervical cerclage.