To determine the morbidity of cervical intraepithelial neoplasia 2+ (CIN2+ ) and CIN3+ of different human papillomavirus(HPV) subtype infection combined with different cytology status. The Shenzhen Cervical Cancer Screening Trial Ⅰ & Ⅱ (SHENCCASTⅠ&Ⅱ) are population-based cross-sectional cervical cancer screening studis conducted in Shenzhen and surrounding area from 2008 to 2010. A total of 12 097 women who aged 25-59 years were included in the analysis. All of these women were detected by liquid-based cytology test and several high-risk HPV-DNA tests. The ones with HPV positive or atypical squamous cells of undetermined sign (ASC-US) were sequentially conducted by cervical biopsy vaginoscopy. Finally, 10 805 samples with complete data of hybrid capture 2(HC2), the polymerase chain reaction-based matrix-assisted laser desorption/ionization time-of-flight assay (MALDI-TOF), HPV genotyping detection, cytology and pathology results were analyzed. The top 6 infection rates of HR-HPV in CIN2+ and CIN3+ were HPV16, HPV52, HPV58, HPV33, HPV31, HPV18. The highest constituent ratio of cytology in CIN2+ and CIN3+ was high grade squamous intraepithelial lesion(HSIL). The morbidities of CIN2+ of patients infected with HPV16, HPV31, HPV58, HPV33, HPV18, HPV52 were 41.3%, 31.5%, 30.6%, 28.7%, 28.2%, 17.7%, respectively, while the morbidities of CIN3+ of those were 33.5%, 20.5%, 19.4%, 15.7%, 19.2%, 8.3%, respectively.The morbidities of CIN2+ in negative intraepithelial lesion or malignancy (NILM), ASC-US, low grade squamous intraepithelial lesion (LSIL), atypical squamous cell cannot exclude high-grade squamous intraepithelial lesion (ASC-H), high grade squamous intraepithelial lesion (HSIL), atypical glandular cell (AGC) samples were 0.4%, 6.9%, 11.1%, 36.4%, 82.0%, 16.7%, respectively, while the morbidities of CIN3+ of those were 0.2%, 3.1%, 4.2%, 22.7%, 64.8%, 0.0%, respectively. The morbidities of CIN2+ in NILM combined with HPV16, HPV18, HPV31, HPV33 infection were 12.6%, 13.3%, 15.8% and 11.5%, respectively, while the morbidities of CIN3+ of those were 10.3%, 11.1%, 7.9% and 7.7%, respectively.The morbidities of CIN2+ and CIN3+ in ASC-US combining with hrHPV infection were high, and the top 6 subtypes associated with high risk of CIN2+ were HPV31 (35.7%), HPV33 (26.9%), HPV16 (26.5%), HPV58 (22.4%), HPV52 (18.6%), HPV68 (15.4%), while those associated with high risk of CIN3+ were HPV16 (20.4%), HPV31 (14.3%), HPV33 (11.5%), HPV58 (8.6%), HPV68 (7.7%), HPV52 (5.8%). Cytology combined with HPV genotyping detection can more effectively estimate the morbidity risks of CIN2+ and CIN3+ . Both high prevalence rates and high risks associated with CIN2+ and CIN3+ of HPV31, HPV33, HPV52 and HPV58 are observed. NILM and ASC-US status combined with these subtypes mentioned above are advised to be conducted by colposcopy.