Objective: To explore the differences in the distribution of vaginal microbiota in perimenopausal women before and after Femoston treatment and compared with healthy women. Methods: A total of 29 perimenopausal patients (study group) who visited the Menopausal Endocrinology Joint Outpatient Clinic of the Second Hospital of Shandong University from January 2022 to December 2023 were selected; all received Femoston treatment and were further divided into the pre-treatment group (FMT1 group, n=29) and the post-treatment group (FMT2 group, n=29). During the same period, using convenience sampling and individual matching methods, 32 healthy women were individually matched from the physical examination population of the Health Management Center of the Second Hospital of Shandong University according to age (±2 years) and a ratio of 1∶1 to 1∶1.1 as the healthy control group. Secretions from the fornix were collected from the FMT1 group, FMT2 group, and control group, and sequenced using 16S rDNA amplicon sequencing technology to analyze microbial Alpha diversity, Beta diversity, intergroup species differences, and biomarkers. Results: The age of the study group was (46.1±6.0) years, and that of the healthy control group was (44.3±3.2) years, with no significant difference (P>0.05). Alpha diversity analysis showed that the Chao1 index [M (Q1, Q3)] [267.72 (139.27, 318.07) vs 109.67 (31.50, 223.55)] and the Observed-OTUs index [255.00 (131.00, 301.50) vs 109.00 (31.00, 208.00)] of the FMT1 group were both higher than those of the FMT2 group (all P<0.05). There were no significant differences in the Shannon index [2.09 (1.71, 3.49) vs 1.98 (1.09, 2.49)] or Simpson index [0.57 (0.39, 0.80) vs 0.53 (0.38, 0.72)] between the FMT1 group and the FMT2 group (all P>0.05). Beta diversity analysis showed that the microbial community structures were significantly separated between the FMT1 group and the FMT2 group, and between the FMT1 group and the healthy control group, with significant differences (R²=0.025, P=0.003 and R²=0.043, P=0.001, respectively), while no significant separation was observed between the FMT2 group and the healthy control group. Analysis of species differences between groups revealed that at the phylum and genus levels, significant differences in abundance between the FMT1 and FMT2 groups were observed in Firmicutes, Bacteroidota, Atopobium, and Prevotella (all P<0.05). Significant differences in abundance between the FMT2 group and the healthy control group were observed in Proteobacteria, Fusobacteriota, Pseudomonas, Ureaplasma, and Megasphaera (all P<0.05). Analysis of microbial biomarkers showed that the characteristic microorganisms in the FMT1 group were Proteobacteria and Bacteroidota, etc., while those in the FMT2 group were Firmicutes and Lactobacillus, etc. Conclusion: Femoston treatment can improve the distribution of vaginal microbiota in perimenopausal women, reduce the diversity of vaginal microbiota and the abundance of various opportunistic pathogenic bacteria genera, and increase the abundance of Lactobacillus.