Background Infection due to HPV (human papillomavirus) is the primary etiology for cervical cancer. Here, we investigated HPV genotypes prevalence and distribution among women in Chongqing, China.Methods Women (total 150639) were recruited from the Department of Gynecology and Obstetrics and Health Management Center, First Affiliated Hospital of Chongqing Medical University in Chongqing Province from January 2014 to December 2019. Cervical samples were conducted for HPV genotyping by testing through a flow cytometry-fluorescence hybridization test.Results All-inclusive HPV prevalence and infection rate in the Health Management Center was 22.3% and 14.4% respectively. Out of the total positive individuals, the rates of single and multiple infections were 77.5% and 22.5%, respectively (the rates of double infections, triple infections, and quadruple or more infections were 17.1%, 4.1%, and 1.3%, respectively). The most frequent genotypes for high risk (HR-HPV) were HPV 52, 16, 58, 53, 56, 39, and 18 in the same sequence, while the most frequent low risk (LR-HPV) genotypes were HPV 61, 81, 43, 44, and 6 in this sequence. For overall and multiple infections of HPV, two peaks for the frequencies were observed on age subgroup analysis, one of these peaks represented women group under 25 years, and the other represented that over 55 years of age.Conclusion Our survey showed that HPV prevalence among women in Chongqing was associated with age and was as high like in other large Chinese cities. Our data provide information for HPV screening and estimating vaccines in this region.