Objective: Compound traditional Chinese medicine (CTCM) with the application of compatibility from multiple active ingredients with multiple?specific targets can achieve a synergistic effect on cancer therapy. This study is aimed to observe the compatibility effects of Aidi injection on the treatment of hepatocellular carcinoma and to explore the mechanism of CTCM. Methods: Aidi injection is a clinical compound prescription containing Mylabris, Ginseng, Astragalus, and Acanthopanax, which can inhibit tumor growth and induce apoptosis. In this study, the anticancer activity of Aidi injection, as well as its disassembled and combined compositions, had been evaluated by varying levels of polyamine biomarkers on human hepatoma Hep?G2 cells detected using ultrahigh?performance liquid chromatography?tandem mass spectrometry. Results: According to the different variations in polyamine levels, it was revealed that Mylabris and Ginseng had an antitumor effect, while Astragalus acted as an assistant and Acanthopanax had weak anticancer activity. The increased level of polyamines in Hep?G2 cells had been found in HL?7702 cells. On combining Mylabris and Ginseng, polyamine levels went close to the normal level, which was even more marked when Astragalus was added. Aidi injection acted like the combination of Mylabris, Ginseng, and Astragalus. Conclusions: This study established a quantitative evaluation of the compatibility effects of Aidi injection based on polyamine biomarkers and evaluated the consistency of its anticancer effect, providing a manner to research the efficacy evaluation of CTCM. Moreover, the correlation between polyamine metabolism and anticancer activity can be used in anticancer drug screening.