Human papillomavirus (HPV) infection is one of the most common sexually transmitted diseases. After studied 602 unvaccinated Chinese women using 16sRNA to detect cervical-vaginal microecology, we analyzed the relationship between HPV infection and vaginal microecology including 20 HPV types. In the vaginal microenvironment of Chinese women, Lactobacillus gasseri and Lactobacillus jensenii were extremely absence, while the ratio of co-exist of Lactobacillus crispatus and Lactobacillus iners increased. Microbial alpha diversity was found significantly higher in the HPV infection and CIN diagnosed groups, compared with healthy control group. Certain bacteria were associated with HPV infection and CIN diagnosed, including Streptococcus, Prevotella, Chlamydia, Bifidobacterium, Ralstonia and Aerococcus. There was no significant change in HPV infection rates between non-Lactobacillus-dominant group and Lactobacillus-dominant group.