Chemotherapy induces inevitable adverse effects, while complementary and alternative medicine employs many chemical substances. Herb pairs normally contain two herbal medicines, and they have satisfactory effects on cancer therapy. Zuojinwan, a well-known herb pair, is composed of Coptidis Rhizoma and Euodiae Fructus. Berberine and evodiamine are considered the most important compounds in the Zuojinwan herb pair. Previous reports have shown that combined use of evodiamine and berberine displays synergistic anticancer activities in various types of cancers, but this combination has not been tested in colorectal cancer. Hence, this study aimed to explore the combined effects of evodiamine and berberine on colorectal cancer cell lines and cardiomyocytes. We found that the combination of berberine and evodiamine showed synergistic anticancer activity in P-glycoprotein (P-gp)-positive colorectal cancer cells through attenuating the overexpression of P-gp mRNA independent of cell cycle arrest and cell apoptosis. However, berberine did not increase the cytotoxicity of evodiamine in normal human colon mucosal epithelial cells. Furthermore, berberine attenuated evodiamine-induced cardiotoxicity by regulating extrinsic apoptosis via nuclear factor erythroid-2-related factor 2 (Nrf2)-dependent and reactive oxygen species-independent pathways. Therefore, we suggest that the combination of berberine and evodiamine displays high anticancer activity while reducing the side effects in specific cell lines.