This retrospective cohort study in Fujian Province aimed to investigate the prevalence and characteristics of non-16/18 HPV infections and their correlation with cervical lesions. Data from 101,621 patients (24,924 HPV positive) over 2012-2022 were analyzed. HPV genotypes, age-specific rates, and cervical pathology were assessed in 11,666 patients undergoing pathological exams. The results revealed that non-16/18 HPV infections, particularly HPV 52, 58, 53, 51, and 81 (with prevalence rates of 5.6%, 2.6%, 2.4%, 2.3%, and 2.2%, respectively), were widespread in the region. The main infection type was single infection rather than complex infection. The age distribution of subgroups with non-16/18 HPV infections shows variations over time, with different peak infection rates across the years. The highest prevalence of non-16/18 HPV infections was observed in patients with low-grade squamous intraepithelial lesions (LSIL). Conversely, HPV16/18 infections were more likely to cause high-grade squamous intraepithelial lesions (HSIL) and cervical cancer. Although the 9-valent HPV vaccine was found to provide broad protection against HPV infections, it did not cover certain non-16/18 HPV types, such as HPV53, HPV51, and HPV81, which remained prevalent. This study aids in optimizing cervical lesion detection and enhancing cervical cancer risk management for non-16/18 HPV infections in Fujian.