Background and aimsHuman papillomavirus (HPV) infection is widespread. The regional differences in infection rates and dominant HPV types are a significant aspect of the virus’s epidemiological characteristics. In China, these differences are further influenced by the country’s diverse ethnic composition, as well as varying economic and cultural conditions across regions. Additionally, factors such as population migration contribute to the exacerbation of these regional disparities in HPV infection rates.MethodsWe conducted an analysis of the current prevalence of HPV among 108,863 patients in Chongqing from 2017 to 2022, along with an investigation into the interaction between HPV and vaginal microbiota. Additionally, we explored the relationship between HPV clearance time and disease outcomes.ResultsOur findings revealed an overall HPV positive rate of 30.14% (32,813/108,863) in Chongqing, China. The top five HPV positive rates were as follows: HPV52 (7.78%), HPV16 (5.85%), HPV58 (4.41%), HPV53 (3.17%), and HPV39 (2.47%). The age-related trend of HPV infection exhibited a bimodal curve. Importantly, the positive rate of high-risk HPV (BV: 24.74%, AV: 24.38%, VVC: 18.19%, TV: 22.81%) was significantly higher than those in the control group (all P<0.05). Follow-up for 4 years, we observed an overall clearance rate of HPV at 92.20%, with a median clearance time of 13 (1-61) months.ConclusionThese findings hold significant implications for the Chinese government in evaluating the prevalence of HPV in the Chongqing region and formulating effective HPV prevention strategies. Moreover, these findings could contribute to the enhancement of public health initiatives related to HPV in the region.