Background <p>Capecitabine (CAP) is widely used in cancer treatment for its oral convenience and tumor targeting. However, its effectiveness in hepatocellular carcinoma (HCC) is suboptimal, possibly due to metabolic enzyme expression differences. This study aims to analyze these enzymes’ expression differences and explore their correlation with clinical pathological factors, to inform personalized CAP treatment.</p> Methods <p>This retrospective study used Immunohistochemistry (IHC) to analyze tumor and non-tumorous samples from HCC patients for CAP metabolic enzyme expression. PRM protein quantification was performed on 10% of samples to validate IHC results. Clinical and pathological data were collected, and multivariable linear regression was used to identify independent risk factors.</p> Results <p>This study analyzed 60 HCC patients with hepatitis B and cirrhosis, revealing significant differences in CAP metabolic enzymes expression between tumor and non-tumorous tissues, with greater individual differences in tumors. Cytidine deaminase (CDA) levels in tumors decreased as liver function deteriorated (<i>P</i> = 0.023), while thymidine phosphorylase (TP) levels increased (<i>P</i> &lt; 0.001). Tumor tissue had lower levels of carboxylesterase 1–2 (CES1-2), CDA, and dihydropyrimidine dehydrogenase (DPYD) but higher TP levels than non-tumorous and normal liver tissues. In tumor tissue, CDA (CV: 118.70%, SD: 3.897) and CES2 (CV: 94.90%, SD: 2.910) showed the greatest individual variability. Multivariable linear regression identified independent risk factors affecting CAP metabolic enzyme expression.</p> Conclusion <p>This study has found significant variability in the expression of CAP metabolic enzymes across individuals and tissues. Developing a treatment flowchart based on metabolic enzymes provides a foundation for personalized HCC treatment and enhances the effectiveness of CAP therapy.</p> <p><i>Clinical Trial Number</i>: Not applicable.</p>