In this paper, the carboxylic multi-walled carbon nanotube (MWCNTs-COOH) was modified with hyperbranched polyester via surface graft, and then the epoxy/MWCNTs-COOH composites were prepared to explore the influences of surface modification of MWCNTs-COOH using hyperbranched polyester on the mechanical performance of the composites. The results of TGA and FT-IR of the grafted MWCNTs-COOH (named MWCNTs-H20) indicated that the hyperbranched polyester was successfully grafted onto MWCNTs-COOH by esterification reaction between carboxyl groups on the surface of MWCNTs-COOH and the hydroxyl groups of hyperbranched polyester. The results of fluorescence microscope elucidate that compared with raw MWCNTs-COOH, the grafted MWCNTs-H20 receives a better dispersion in the epoxy prepolymer. Moreover, MWCNTs-COOH and MWCNTs-H20 were, respectively, added into epoxy prepolymer to prepare the EP/MWCNTs composites. The results of DMA revealed that the addition of MWCNTs-COOH enhanced the low temperature toughness of the neat EP, and the surface grafting of hyperbranched polyester onto MWCNTs-COOH further decreased the glass transition temperature of the composites and exhibited a better performance in the enhancement in toughening EP. The measurement of the mechanical performances and surface morphology revealed that the addition of MWCNTs-H20 enhances tensile strength, elongation at break and Charpy impact strength of the EP/MWCNTs composites significantly, resulting in a better toughness of the composites; however, it had little influence on the Barcol hardness.