Abstract:[Background] human papillomavirus (HPV) infection is closely related to cervical cancer and precancerous lesions. HPV vaccine is an important means to prevent infection, but the distribution of HPV subtypes has obvious regional differences. [Objective] To acquaint with the current situation of cervical HPV infection in women in Western Sichuan Plateau, and to explore the relationship between HPV infection and vaginal microenvironment changes, which could provide guidance for the use of HPV vaccine and the prevention of cervical cancer to them. [Methods] A total of 3 816 women in plateau area of Western Sichuan in 363 Hospital between November 2017 to May 2019, were selected for HPV genotyping, thinprep cytologic test (TCT) and vaginal microenvironment examination at the same time. The infection rate and genotype distribution of HPV were analyzed, and the relationship between high risk HPV (hrHPV) infection and vaginal microenvironment was discussed. [Results] Among 3 816 women in Western Sichuan Plateau, the total infection rate of HPV was 19.81% (756/3 816), and the infection rate of hrHPV was 16.48% (629/3 816). The highest proportion of hrHPV was HPV52, which was 17.20% (135/785), followed by HPV58 (92/11.72%), HPV16 (89/11.34%), HPV53 (88/11.21%) and HPV18 (55/7.01%). Among 415 cases of cervical cytopathy, 101 cases (24.3%) were infected with hrHPV. The top five subtypes were HPV52/58/16/18/31. The top five of high cytopathic hrHPV infections were HPV52/58/18/31/16, and the top seven of low cytopathic hrHPV infections were HPV58/16/56/53/52/68/51 . Among 1 696 cases of vaginal microenvironment changes, the infection rate of hrHPV was 19.16% (325/1 696), which was higher than that of normal vaginal microenvironment (P<0.05). Bacterial vaginitis (BV) was associated with hrHPV infection (P<0.05), while leukocytosis alone, vulvovaginal candidiasis (VVC), trichomonal vaginitis (TV) and mixed infection were not associated with hrHPV infection (P>0.05). [Conclusion] The infection rate of HPV and hrHPV in women living in Western Sichuan Plateau are higher. The top five subtypes of hrHPV are HPV52/58/16/53/18, and the top five subtypes of hrHPV with cervical cytopathy are HPV52/58/16/18/31. 9-Valent Human Papillomavirus Vaccine may be more suitable for the prevention of HPV infection and cervical cancer in this area. HPV53, which is common in this area, may cause cervical cytopathy, but there is no vaccine available. Therefore, HPV53 may be one of the domestic HPV vaccine development targets. Moreover, BV may be associated with hrHPV infection, so BV infection patients might be one of the key points of cervical cancer prevention and control.