Objective To investigate the distribution of human papilloma virus （HPV） genotypes and analyze the impact of HPV infection on vaginal vault epithelial cell lesions. Methods A total of 191 patients with positive HPV genotyping results from exfoliated vaginal stump cells after hysterectomy at Yancheng Maternal and Child Health Care Hospital Affiliated to Yangzhou University （January 2021-December 2024） were retrospectively analyzed. The HPV genotype distribution and its correlation with vaginal cell lesions were statistically analyzed. Results Twenty-three HPV subtypes were detected in the 191 patients. The top six high-risk HPV genotypes were 52，16，58，31，51，and 18 subtypes. Single-type，dual-type，and multiple-type infections accounted for 102 （53.40%），54 （28.27%），and 26 （13.61%） cases，respectively，with one patient infected by six subtypes. Colposcopy results revealed that there was no intraepithelial lesion or malignancy（NILM）in 73 cases（38.22%），while there was vaginal intraepithelial neoplasia （VaIN） grade I in 95 cases （49.74%），gradeⅡn 20 （10.47%），and gradeⅢin 3 （1.57%）. The number of HPV subtypes showed no statistically significant correlation with hysterectomy indications or vaginal vault epithelial pathology degree. However，HPV16 infection in vaginal stump was significantly associated with the degree of vaginal vault epithelial pathology. Conclusions The genotypes of HPV infection in vaginal stump are distributed differently in different regions. It is recommended that women in Yancheng area should give priority to HPV 9 vaccine，and HPV-infected patients should be properly treated，especially HPV16-positive patients，who should receive timely TCT and colposcopy in a standardized manner for early diagnosis and treatment of VaIN.