Objectives: This study investigated and compared the prevalence and distribution of high-risk human papillomavirus (HR-HPV) genotypes in Tongliao and Huidong regions of China. Materials and methods: A cross-sectional study of the results of cervical cancer screening was conducted between August 2017 and April 2018 in Tongliao, Inner Mongolia as well as Huidong, Sichuan Province, China. Totals of 2351 and 1583 women recruited in Tongliao and Huidong, respectively, who underwent cytology sampling, collected for thinprep cytologic tests (TCT) and PCR-based HPV genotyping tests. Participants whose HPV and TCT results met relevant indications were referred for colposcopy. Results: The overall prevalence in the Tongliao and Huidong cohorts were 19.35% and 10.4% (P 0.05), among which the five most common genotypes were HPV16 (3.91%), 52 (3.79%), 53 (2.42%), 68 (2.04%), and 51 (1.96%) in Tongliao and HPV52 (2.27%), 16 (1.58%), 58 (1.39%), 51 (1.39%), and 53 (0.95%) in Huidong. In both cohorts, single-type infections were more common than multiple-type infections. HPV16 was the most common genotype in high-grade squamous intraepithelial lesions. In the Tongliao cohort, HPV33, HPV52, and HPV58 showed a risk of carcinogenesis similar to HPV18. Conclusions: This study provides information on HPV prevalence and genotype distribution in Tongliao and Huidong. The HPV prevalence and genotype distribution were found to differ geographically. The HPV genotyping tests provided more details, which can be instructive and meaningful for both the prevention and management of HPV infection and cervical lesions.