Women with normal pathology screened from abnormal cervical cytology are a special population with higher progression risk than women with normal cytology. However, the associations between genotype distribution and changes of high-risk human papillomavirus (HR-HPV) infection and cervical progression risk in this special population remain unclear. A total of 1232 women with normal pathology screened from abnormal cervical cytology were enrolled into this cohort with 2-year follow-up. HPV genotyping detection was performed through flow-through hybridization. Hazard ratios (HRs) and Odds ratios (ORs) were calculated using Cox proportional hazard regression and logistic regression models, respectively. Overall HR-HPV prevalence at baseline was 29.0%, with HPV16, 52, 58, 53 and 51 the top five genotypes. The 2-year persistence rate of HR-HPV infection was 31.9%. Compared with HR-HPV negative, the adjusted HRs of overall HR-HPV, HPV16, 31/33, 58, 51, and 53 infections for the progression risk of normal cervix were 5.31, 7.10, 6.95, 5.74, 5.04, and 4.88, respectively. Multiple HR-HPV infection cannot lead to an additional risk of progression relative to single HR-HPV infection. In comparison with HR-HPV persistently negative, same-type HR-HPV persistence was positively associated with progression risk of normal cervix (adjusted OR: 22.26), but different-type HR-HPV persistence was not linked to cervical progression. Genotypes and persistence of HR-HPV infection could stratify the cervical progression risk in women with normal cervical pathology and abnormal cytology and provide evidence for development of next generation of vaccines. HPV51 and 53 deserved attention apart from HPV16, 31, 33, and 58.