Background HPV persistent infection is a strong carcinogenic factor to induce cervical cancer. Investigation of HPV epidemiology and genotype distribution is meaningful for the development cervical cancer prevention and control strategies. Methods By using PCR-based hybridization gene chip assay, HPV genotype was detected of 14185 women that came from HEC (Health Examination Center) or OGOC (Obstetrics and Gynecology Outpatient Clinics) between 2015 and 2017 in Sichuan area. The epidemiology and genotype distribution as well as the relationship to in histology and cytology abnormalities were analysed. Results The positivity of HPV was 23.84%. The HPV-positive rate of OGOC group (37.62%) is significantly higher than that of HEC group (15.29%), p <0.05. The prevalence of HPV reached peak at 41-50 age (5.86%) in HEC group, but at 21-30 age (14.74%) in OGOC group. Of the HPV positive women, single genotype infection was the most common form in both HEC and OGOC group, accounted for 62.06% in total screening population, 74.36% in HEC group and 54.01% in OGOC group. Three most prevalent HPV types were HPV-52 (5.02%), 58 (3.61%), 16 (3.24%) in total screening population. Of the HPV positive women, the top three were HPV-52 (20.93%), CP8304 (15.32%), 58 (14.42%) in HEC group, while were HPV-52 (21.14%), 16 (16.34%), 58 (15.61%) in OGOC group. HPV 52/16/58 accounted for the 41.84% of cytology and 56.52% of histological abnormalities. Conclusions Women in Sichuan area are facing with the great threat of HPV infection, especially the women of 21~30 or 41-50 years old. HPV 52, 58, 16 were the priority HPV type in OGOC group, while in in HEC group is HPV 52, CP8304, 58. HPV 52/16/58 accounted for the majority of cytology and histological abnormalities. These accurate data could provide a scientific basis for the prevention and control strategies of cervical cancer in Sichuan area.