To determine the role of vaginal microbiota in the efficacy of cervical cerclage in obstetric outcomes of twin pregnancies. 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. 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 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). A healthy vaginal environment is essential to improve the obstetric outcome for twin pregnancies with cervical cerclage.