This dataset included 5063 T cells from tumor tissues, normal tissues, and peripheral blood of six HCC patients that had been assigned to 11 T cell subsets including naïve T cells (C01_CD8.LEF1, C06_CD4.CCR7), effector T cells (C02_CD8.CX3CR1, C11_CD4.GNLY), exhausted T cells (C04_CD8.LAYN, C10_CD4.CXCL13), Tregs (C07_CD4.FOXP3, C08_CD4.CTLA4), mucosal-associated invariant T cells (C03_CD8.SLC4A10), and intermediate T cells (C05_CD8.GZMK, C09_CD4.GZMA). This evidence concerns the gene CX3CR1 and hepatocellular carcinoma.