Recurrence and metastasis remain the major obstacles to prognosis of hepatocellular carcinoma (HCC), but the relationship between phosphoproteomics and drug targets need to be studied more systematically. In this study, we performed the phosphoproteomics data collected from 18 paired HCC patients to establish the phosphoproteomics profiles of HCC and provide an important resource to explore the relationships between protein phosphorylation and drug targets in HCC. Our data bring new insights on multi-omics data and have the potential to further understand the relationship between post-translational modification (PTM) levels of proteins and different molecular and clinical features of HCC patients. XAD1—XAD18 --- HCC adjacent normal tissues XC1—XC18--- HCC tumor tissues