Objective: To screen out key differentially expressed methylation genes in hepatocellular carcinoma (HCC) by extracting data from the NCBI-GEO and TCGA databases, discuss the interaction of key genes in HCC and explore the influence of these genes on tumor progression.Methods: The clinical information and sequence data of HCC patients and healthy controls were extracted from the NCBI-GEO and TCGA databases. The module that presented the highest correlation with the tumor phenotypes was selected by the WGCNA network and TOM analysis. GO and KEGG analyses were used for signaling pathway analysis. Key differentially expressed genes were screened out from the module. KM plot analysis was performed to determine the impact of key genes on patient survival. The relationship between core genes and tumor immune infiltration was also discussed. Drug sensitivity analysis was performed to observe the sensitivity of key genes methylated by chemotherapeutic drugs and thus determine the associated effects on patient prognosis. Finally, the molecular mechanisms of the genes involved in tumor progression were analyzed by GSVA, and the interactions between key genes were revealed using Gene MANIA analysis.Results: A total of 373 differentially expressed genes were screened, including 88 upregulated genes and 285 downregulated genes. Three of these genes, CHST4, CRHBP, and IGFBP3, were found to be abnormally methylated in HCC patients and significantly associated with expected survival. The relationship between these key genes and tumor immune invasion was confirmed, and these genes play a protumor or antitumor role through immune cell mediation. In addition, we found that CHST4 and IGFBP3 expression can significantly reduce the sensitivity of several commonly used chemotherapy drugs to tumor cells, while CRHBP expression plays a synergistic role with chemotherapy drugs to enhance mutual effects. The participation of these genes in specific signaling pathways involved in liver metabolism and tumor progression has also been identified. Finally, complex interactions between the three core genes and other related genes were presented.Conclusion: The CHST4, CRHBP and IGFBP3 genes present significant methylation and differential expression in HCC, are involved in tumor immune infiltration, and affect chemotherapy drug sensitivity. As potential biomarkers and therapeutic targets, they may be beneficial to the diagnosis and prognosis of HCC patients in the future.