In this paper, carboxylic multi-walled carbon nanotubes (MWCNTs-COOH) were modified by a series of hyperbranched polyesters (HBP) with different molecular structures (different branching degree) through surface grafting, and then the epoxy resin (EP)/carbon nanotube composites were prepared to explore the influences of structure regulation of HBP modified carbon nanotubes on the toughening performance of the composites. The results of Fourier transform infrared spectroscopy (FTIR), transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), and thermogravimetric analysis (TGA) of various HBP grafted carbon nanotubes confirmed that the HBP were successfully grafted onto MWCNTs-COOH an esterification reaction between the carboxyl groups of MWCNTs-COOH and the hydroxyl groups of HBP, meanwhile, the higher the branching degree of the HBP, the higher its grafting ratio onto carbon nanotubes. Furthermore, the outcome of dynamic thermal mechanical analysis (DMA) indicated that the addition of MWCNTs-COOH increased the storage modulus and glass transition temperature ( ) of the pure EP, and surface grafting of various HBP onto MWCNTs-COOH decreased the and peak height of mechanical loss of composites. And as the branching degree of HBP increased, the interfacial bonding between MWCNTs and the EP matrix became stronger. The results of mechanical performance and morphology analysis also revealed that the addition of HBP grafted MWCNTs-COOH significantly improved its dispersion and interfacial bonding in the EP matrix, resulting in better performance in the enhancement of toughness of the composites. In addition, it was found that the higher the branching degree of HBP, the better the toughening performance of the composites.