Objective:To evaluate the characteristics of vaginal flora between normal and abnormal pregnant women throughout pregnancy.Methods:Vaginal swab specimens were collected from pregnant women in the first (<14 gestation weeks, GW), second (14~28 GW) and third trimester (>28 GW) in Anqing, Anhui Province from February 2018 to February 2020. Pregnant women were divided into normal and abnormal groups according to all clinical diagnosis. The sequences of 16S rRNA gene (V3-V4) from vaginal swabs were analyzed using QIIME2 platform. The differences in the dominance of Lactobacillus, community state type (CST) transition, Alpha diversity and Beta diversity were analyzed. Diversity data after log transition were used in the analysis of linear mixed model. Results:A total of 34 pregnant women (10 normal and 24 abnormal) with 102 samples were included for analysis. The composition of vaginal flora between two groups: the relative abundance of Lactobacillus was the highest at the genus level and Lactobacillus crispatus and Lactobacillus iners was the top two species with high relative abundance. The dominance of Lactobacillus, Alpha diversity and transition of CST were also similar. Both groups had a gradually decreased trend of Alpha diversity with GW, and the Chao1, Observed species and Faith′s PD indexes′ were different in different GW ( P<0.05). All Beta diversity metrics in normal group had descending trend, with lower value of the index of first distance which implied a higher microbiota stability, while Bray-Curtis, Weighted UniFrac distance had ascending trend in abnormal group, indicating lower stability. Jaccard distance′s first distance was statistically differed among GW and Unweighted UniFrac distance′s differed between normal and abnormal groups. Conclusions:The first distance of Unweighte UniFrac distance in abnormal pregnant women is higher than that of normal pregnant women and the vaginal flora in abnormal group has lower stability.