The purpose of this study was to compare the structural composition of vaginal microbial community between women with vulvovaginal candidiasis and healthy women, and to analyze the relevance between dominant bacteria and vulvovaginal candidiasis. A total of 18 patients with vulvovaginal candidiasis (VVC group) and 27 healthy women (NC group) were recruited. The VVC group received clotrimazole treatment, while the NC group received no treatment. The vaginal secretions of the NC group were collected once, and those of the VVC group were collected four times (before treatment and on the 10th, 30th, 60th days after treatment). Total DNA in the vaginal secretions samples was extracted respectively. The bacterial diversity in the vaginal secretions samples was analyzed using high-throughput sequencing technology. Changes in the bacterial community in the VVC group of the vaginal secretions samples before and after treatment were discussed, and the difference in the bacterial community was compared with the NC group. The results showed that the dominant vaginal bacteria in the VVC group were primarily Lactobacillus iners, while Lactobacillus crispatus dominated in the NC group. After treatment with clotrimazole, no significant difference was observed in the vaginal microbiota composition of the VVC group compared to pre-treatment. This study confirms that vaginal bacterial community composition of patients with vulvovaginal candidiasis is significantly different from that of healthy women. Clotrimazole treatment for vulvovaginal candidiasis can not promote the transformation of vaginal dominant bacterial community to a healthy state.