To explore the underlying risk factors and to prevent misdiagnosis of cervical intraepithelial neoplasia (CIN) coexisted with vaginal intraepithelial neoplasia (VaIN). Clinical data of patients pathologically diagnosed with CIN were collected from January 2017 to December 2018. A total of 446 cases were analyzed, including 406 cases of single lesions ('CIN single' group) and 40 cases complicated with VAIN ('VAIN concurrent' group). The median age of the VAIN concurrent group was 53years (46.25-59years), and the median age of the CIN single group was 44years (36-50years). Regarding menopausal status, there were 28 cases (70.0%) in the VAIN concurrent group and 89 cases (21.9%) in the CIN single group (P < 0.005). The median load of high-risk human papillomavirus (Hr-HPV) in the VAIN concurrent and CIN single group was 923.4 relative light units/cutoff (RLU/CO) (145-2172.2 RLU/CO) and 229.155 RLU/CO (18.615-638.1275 RLU/CO), respectively (P = 0.037). The results revealed that the menopausal status was an independent risk factor for VAIN occurrence in CIN patients. The risk of VAIN in menopausal patients was higher than that in non-menopausal CIN patients (OR = 8.311, 95% CI 4.062-17.005). Age and HPV load were also related to the concurrence of VAIN and CIN. Examinations regarding vaginal screening are of great importance in the diagnosis of perimenopausal and postmenopausal CIN patients, especially patients with Hr-HPV load. Colposcopy and tissue biopsy should also be performed, when necessary, to avoid misdiagnosis and the appearance of vaginal lesions.