Objective　To investigate the relationship between the degree of cervical lesions and the status of paired box-1 (PAX1) and tumor protein 63(TP63) gene promoter methylation in human papillomavirus (HPV)-positive patients with cervical lesions, as well as analyze their clinical significance. Methods Cervical tissue specimens were collected from 128 patients who were suspected of cervical lesions and HPV infection, and admitted to Qionghai People&#39;s Hospital between December 2021 and December 2022. According to pathological examination results, the patients were divided into the low-grade squamous intraepithelial lesion (LSIL) group (n=43), high-grade squamous intraepithelial lesion (HSIL) group (n=51) and cervical cancer group (n=34). The second-generation hybrid capture method was used for viral load. The degree of PAX1 and TP63 gene promoter methylation in each group was detected by bisulfite sequencing, and mRNA expression of PAX1 and TP63 was detected by real-time quantitative PCR. The diagnostic performance of the degree of PAX1 and TP63 methylation for cervical intraepithelial neoplasia (CIN2+) was evaluated. Results There were statistically significant differences in HR-HPV viral load between the groups (P>0.05). A total of 49 (38.28%) patients with PAX1 gene promoter methylation, and 55 (42.97%) patients with TP63 gene promoter methylation were detected among the 128 patients. The percentages of PAX1 and TP63 gene promoter methylation in the cervical cancer group, HSIL group and LSIL group were (67.65% and 73.53%), (43.14% and 49.02%) and (9.30% and 11.63%), with statistically significant differences between groups (P<0.05). The mRNA expression levels of PAX1 and TP63 in the cervical cancer group, HSIL group and LSIL group were [(0.34±0.08) and (0.45±0.13)], [(0.72±0.11) and (0.63±0.09)], [(1.04±0.09) and (0.87±0.11)], with statistically significant differences between groups (P<0.05). Receiver operating characteristic (ROC) curve analysis showed that the area under the curve (AUC) values of PAX1, TP63 gene promoter methylation, and their combination for diagnosing CIN2+ were 0.793, 0.842, and 0.857, respectively. The sensitivity values were 77.78%, 83.33%, and 77.78%. The specificity values were 80.85%, 85.11%, and 93.62%. The combined detection can improve the specificity of diagnosis of CIN2+ lesions. Conclusions The degree of PAX1 and TP63 gene promoter methylation is closely related to cervical lesions in patients with HPV infection, which indicates that it can be used as potential auxiliary indicators for the clinical diagnosis of CIN2+lesions.