Previous clinical studies have shown the safety and efficacy of the traditional Chinese medicinal herbal aqueous extract Chan-Yu-Bao-Yuan-Tang (CYBYT) for the treatment of lung and cervical cancer patients. Used in combination with 5-fluorouracil (5-Fu), CYBYT has been observed to be particularly effective in cancer treatment. Herein, the combined anticancer effect and the underlying mechanisms of 5-Fu and CYBYT in the human lung cancer cell line A549 and the human cervical cancer cell line HeLa were investigated in vitro. The MTT assay, Annexin V-FITC staining and Western blotting were applied to identify cell viability, the stages of apoptosis and the expression of signaling proteins, respectively. The results indicated that CYBYT and 5-Fu, alone or in combination, significantly inhibited proliferation and induced marked apoptosis in A549 and HeLa cells, but had no significant inhibitory effects on normal human IMR-90 fibroblasts. The rate of mid and late apoptosis or necrosis was greater after 5-Fu treatment compared to treatment with CYBYT or the combination of agents; however, the early apoptotic rate showed opposite results. CYBYT and 5-Fu, alone or in combination, up-regulated cleaved caspase-3 expression in a time-dependent manner, with CYBYT being more effective than 5-Fu. Taken together, our data show that the pro-apoptotic activity of the two-drug combination was much stronger than that of CYBYT or 5-Fu alone; CYBYT combined with 5-Fu had synergistic effects at lower concentrations and promoted apoptosis, while the combined treatment also decreased the cytotoxic side effects of 5-Fu.