Many microorganisms live in the vagina of healthy women. They interact with and compete with the microenvironment in the female vagina to form a dynamic balance of the microenvironment in the female vagina. However, imbalanced vaginal microecology can lead to vaginal resistance to pathogenic microorganisms. Poor capacity can cause women to develop infections of the reproductive tract. This article analyzes the vaginal microecological status of women with high-risk HPV infection for more than 6 months and healthy women and explores the risk factors that cause long-term high-risk HPV infection for timely detection and regulation of possible vaginal microecological imbalance in women with high-risk HPV infection for more than 6 months to prevent further development of cervical lesions in such patients. This article covers women with a sexual life history who attended the gynecology department of a hospital from January 2020 to September 2021. There were 280 patients in the experimental group: positive high-risk HPV; and there were 140 patients in the control group: negative high-risk HPV test. The correlation between vaginal microecology of CIN patients and patient prognosis according to the subject's vaginal microecology test results and prognosis of various levels of cervical lesions was analyzed. The experiment proved that the detection rate of normal vaginal microecology in the experimental group was 12.14% (34/280) compared with the detection rate of 29.29% (41/140) in the control group, and there was a trend of decrease, and the difference was statistically significant (χ2 = 17.23, P < 0.05). The detection rate of vaginal BV in the experimental group was 10.36% (29/280) compared with the detection rate of 5.0% (7/140) in the control group, and the difference was statistically significant (χ2 = 5.19, P < 0.05). This indicates that women with high-risk HPV infections for 6 months or longer have a higher incidence of vaginal microecological imbalances than healthy individuals and aggressive vaginal microecological screening. It is necessary to carry out the program. Detect and treat possible abnormal conditions in time to prevent the further onset of the disease.