The present study identified six hub targets—GOT1, CYP2C9, CYP34, CYP1A2, CA2, and ABAT—that are involved in five core pathways related to HQD’s effects on malignant progression in colorectal cancer liver metastases, integrating transcriptomic and metabolomic analyses. This evidence concerns the gene CYP2C9 and colorectal cancer.