pH-Responsive aptamer-linked DNA nanostructures can actively target cancer cells to release drugs in the cells’ acidic environment. Tea polyphenols can be used as cancer-preventive agents to enhance the efficacy of chemotherapeutic drugs. In this study, we constructed a pH-responsive DNA tetrahedron with MUC1 aptamer (MUC1-TD) to co-load irinotecan hydrochloride (CPT-11) and (-)-epicatechin (EC). The thermodynamic parameters for the interaction of CPT-11 and/or EC with MUC1-TD were investigated using fluorescence spectroscopy and calorimetry. The binding of CPT-11 to MUC1-TD was found to be stronger than that of EC. Differential scanning calorimetry and fluorescence quenching experiments demonstrated the intercalative binding between CPT-11/EC and MUC1-TD. The in vitro release rate of CPT-11 was faster at pH 5.0 than at pH 7.4, confirming the pH-responsive of MUC1-TD. In vitro cytotoxicity results indicated that CPT-11 loaded by MUC1-TD was more cytotoxic than free CPT-11. Further, we found that the cytotoxicity of CPT-11 was further enhanced in the presence of EC due to a synergy between them. Additionally, cell uptake experiments showed that CPT-11 and EC loaded by MUC1-TD were mainly distributed in the nucleus of human breast cancer cells (MCF-7). These findings indicate that pH-responsive DNA nanostructures are a promising delivery system for co-loading chemotherapeutic drugs and natural polyphenols.