To investigate the correlation between high-risk human papillomavirus (HR HPV)-negative cervical lesions and cervical microenvironment in Inner Mongolia, China, and to find the pathogenic factors of HR HPV-negative cervical lesions. 74 cases of HR HPV-negative healthy women and 80 cases of patients with cervical lesions (28 cases of LSIL, 49 cases of HSIL and 3 cases of CSCC) were selected as the study group; 26 cases of HPV-positive women and 352 cases of patients with cervical lesions (108 cases of LSIL, 214 cases of HSIL and 30 cases of CSCC) were control group. Questionnaires were collected from the study group and the control group and specimens were collected. Gram staining, hematoxylin and eosin staining microscopy, and substrate colorimetry method were used to detect vaginal micro-ecological indicators; ELISA was used to detect the concentration of SIgA, IgG, IL-2 and IL-10 in vaginal lavage fluid. Genetic testing was used to detect HPV, mycoplasma, and chlamydia infection. The changes of vaginal micro-ecology evaluation index and local immune factor concentration in healthy women and cervical lesions of all grades in the study group and the control group were compared. Patients with cervical lesions, compared with healthy women, had a decrease in dominant lactobacilli and dysbacteriosis (P < 0.05), and this trend became more apparent as the disease progressed. The diversity and concentration of the flora in the HPV-negative group increased, the abnormal composition ratio decreased, and the HPV-positive group showed the opposite trend. As the lesion progressed, H This study showed that vaginal micro-ecological imbalance and weakening of local cervical immune function are important reasons for the development of cervical lesions. It is expected to inhibit the development of cervical lesions by regulating the balance of vaginal micro-ecology and enhancing local immune function. By detecting Lactobacillus vaginalis, pre-enzyme, IL-2, IL-10, SIgA, it can guide the further diversion of HPV-positive women and predict the development direction of cervical lesions after HPV infection.