Objective:To explore the relationship between cervical microecology and cervical squamous intraepithelial lesions (SIL).Methods:All subjects were recruited from the health care center or gynecology of the Affiliated Wuxi No.2 People′s Hospital of Nanjing Medical University from March to May of 2019, including 12 subjects normal cervix with 37-47 years old, 21 low-grade squamous intraepithelial lesion (LSIL) subjects with 39-48 years old, 5 high-grade squamous intraepithelial lesion (HSIL) subjects with 38-45 years old and 3 cervical squamous cell carcinoma subjects with 42-43 years old. All subjects were required to fill in a questionnaire, and performed cervical examination. Meanwhile, the microecology of cervical secretions was analyzed by the next generation sequencing (NGS) and the NGS results were analyzed by bioinformatics. Subjects were divided into human papilloma virus (HPV)-negative groups, low-risk HPV (lrHPV), 16/18 high-risk HPV (hrHPV) and other hrHPV infection groups based on HPV test results of NGS. The Venn diagram of data, microecology diversity, the relative abundance and co-occurrence of species, and the receiver operating characteristic (ROC) curve were analyzed.Results:A total of 909 species at the species level were obtained from the cervical secretions of all the subjects, and there was overlap among the groups. There was no significant difference in total HPV infection rate, 16/18 hrHPV infection rate and other hrHPV infection rates among subjects with different cervical lesions (all of P>0.05). Grouped by HPV infection, the 16/18 hrHPV-infected and other hrHPV-infected subjects had increased cervical microecology diversity ( U=39.00 and 43.00, all of P<0.05), and the relative abundance of Lactobacillus crispatus (L.crispatus) had no differences among the groups ( H=4.37, P=0.213 6). Grouped by cervical conditions, the cervical microecology diversity of the subjects with cervical lesions increased ( H=14.60, P=0.002 2), while the L.crispatus relative abundance decreased ( H=13.98, P=0.000 8). Among all the detected species, Mycoplasma, Chlamydia and Streptococcus B had a co-occurrence, while Lactobacillus iners, Gardnerella vaginalis, Atopobium vaginae, and Prevotella bivia had a co-occurrence. As the SIL diagnostic index, the area under the ROC curve (AUC) of the relative L.crispatus relative abundance was 0.874 [95% confidence interval ( CI):0.732-0.957]. L.crispatus combined with Lactobacillus jensenii (L.jensenii) and Mycoplasma had an AUC of 0.943 [95 %CI: 0.822-0.991] in the SIL diagnosis. Conclusions:The decreased L.crispatus relative abundance and the increased cervical microecology diversity may be related to HPV infection and cervical lesions; simplified NGS data may be helpful to the SIL diagnosis.