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Background Common hub genes (CHGs) in gastrointestinal cancers (GICs) and their prognostic potential and immune infiltration in hepatocellular carcinoma (HCC) are limited. Methods Differential analysis of genes in the six GICs was performed, and CHGs were identified using the survival and protein-protein interaction (PPI) network analyses. A polygenic prognostic model was constructed based on the CHGs using the LASSO-Cox regression algorithm and validated in two cohorts. CHGs-related multivariate Cox regression and immune infiltration analyses were performed. Results Ten CHGs (TOP2A, CCNB1, CDK1, MAD2L1, RRM2, CCNA2, BUB1B, CDC6, AURKA, and BUB1) were obtained. In The Cancer Genome Atlas (TCGA) cohort, a 3-gene (CCNB1, MAD2L1, and BUB1) prognostic model was built. A significant difference was showed in the overall survival of patients between the two groups. Moreover, both type I and II interferon response pathways decreased in high-risk HCC patients. These results were also validated in the ICGC and internal cohorts. Conclusions 10 CHGs in six GICs was revealed. In HCC, a prognostic model based on the 3 CHGs in GICs was constructed. Both type I and II interferon response pathways markedly decreased in the high-risk group of HCC patients. This might provide novel perspectives for the targeting and immunotherapy of GICs.