Background: Increasing evidence suggests that both the vaginal microbiota and human papillomavirus (HPV) may play a role in the development of cervical intraepithelial neoplasia (CIN) and cervical cancer. However, the relationship between the vaginal microbiome and HPV infection remains poorly understood. The objective of this study was to investigate the association between indicators of the vaginal microbiota and HPV infection. Methods: From January 2020 to June 2022, clinical data were collected from 5099 outpatients at Beijing Friendship Hospital. These patients underwent simultaneous testing for vaginal microecology and HPV type. A statistical analysis was conducted to examine the relationship between indicators of the vaginal microbiota and HPV infection. Results: HPV infections were detected in 12.47% (636/5099) of the subjects. Single, double, triple, quadruple, and quintuple infections accounted for 81.29%, 14.62%, 3.14%, 0.94%, and 0.15% of all infections, respectively. A significant disparity in HPV infection prevalence was observed between the vaginitis group and the general population. However, no variation was found among different vaginitis groups. The data indicated that individuals with clue cells and sialidase were more susceptible to HPV infection. Sialidase was identified as an independent risk factor for HPV infection in a multivariable logistic regression model. The most prevalent HPV subtypes were 16 and 52, representing 2.10% and 2.86%, 3.14% and 2.86%, 1.78% and 2.16% in the normal, bacterial vaginitis, and other groups, respectively. Conclusions: Our findings demonstrate the presence of clue cells and sialidase, which are two diagnostic criteria for bacterial vaginitis, in association with HPV infection. Furthermore, our results suggest that sialidase could potentially serve as a valuable predictor of HPV infection.