Heterogeneous nuclear ribonucleoprotein E1, also known as hnRNP E1, is an essential RNA-Binding Protein (RBP) that is essential for the growth of tumors. The development of HPV-associated malignancy and the expression of the HPV gene are both influenced by the presence of several RNA/DNA binding sites and various RBPs on the Human papillomavirus 16 (HPV16). It is yet unknown how hnRNP E1 affects HPV16 oncogenes in the growth of cervical lesions. A community-based cohort was established in Shanxi Province, China, with a total of 816 participants who had cervical lesions of various grades. The relationship between the expression of hnRNP E1 mRNA and cervical lesions was examined using data from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. We created cells that have hnRNP E1 up- and downregulated. Cell counting kit-8, analyses from flow cytometry, and chromatin immunoprecipitation sequencing were all used to assess hnRNP E1 functions. Our findings demonstrated that the degree of the cervical lesions had a linear relationship with hnRNP E1 expression. Cervical lesions could be more likely to develop in those with low expression of HPV16 E2, high expression of E6, and a low ratio of E2 to E6. HPV16 oncogene expression and hnRNP E1 expression were associated. Dopaminergic synapses, the Wnt signalling system, gnRH secretion, and the mTOR signalling pathway were all impacted by hnRNP E1-relevant genes. Significantly reducing HPV16 E6 expression, inducing apoptosis, arresting the cell cycle at the G0/G1 stage, and inhibiting cell proliferation were all effects of hnRNP E1. Our findings suggest that hnRNP E1 could suppress the expression of the HPV16 E6 oncogene and prevent cervical cancer development, which provides new insight into how to stop the carcinogenicity of HPV across a variety of diseases by controlling RNA-binding proteins.