To add the growing literature on baseline of high‐risk human papillomavirus (HR‐HPV) genotype distribution in cervical intraepithelial neoplasia (CIN) before the widespread using of HPV vaccines in Chinese mainland and to improve risk stratification of HR‐HPV–positive women. Retrospectively, the data of age, cervical HPV genotypes, cytology, and pathology were collected from 1166 patients who received loop electrosurgical excision procedure (LEEP). HPV genotypes were analyzed with Flowcytometry Fluorescence Hybridization Method. And then HPV prevalence, HR‐HPV genotype distribution and the correlation of HR‐HPV genotypes with CIN2+ (CIN2 or severer) were analyzed. The role of multiple HR‐HPV types infection with or without HPV16/18 in the pathogenesis of CIN2+ was also analyzed. The 6 most common HR‐HPV genotypes were HPV16, 58, 52, 33, 18, and 31 in descending order. Compared to HR‐HPV–negative women, HPV16, 33 or 58 positive women had higher risk of CIN2+ (OR = 5.10, 95% CI = 2.68‐9.70; OR = 3.09, 95% CI = 1.39‐6.84; OR = 3.57, 95% CI = 1.85‐6.89, respectively). And women who were infected by multiple HR‐HPV types infection with HPV16/18 also had higher risk of CIN2+ (OR = 2.58, 95% CI = 1.35‐4.92). However, multiple HR‐HPV types infection without HPV16/18 did not increase the risk significantly (P = .08). Compare to bivalent Cervarix® and quadrivalent Gardasil®, HPV prophylactic vaccine targeting HPV31, 33, 52, and 58 might provide women more protection from HPV‐induced cervical cancer in China. The women who infected by HPV16, 33, 58, or multiple HR‐HPV types with HPV16/18 have higher risk of CIN2+ and need to be paid more attention in screening processes. And the role of multiple HR‐HPV types infection without HPV16/18 needs be further identified in more studies.