The development of a novel accelerator capable of simultaneously enhancing the cross-linking density and ductility of an epoxy resin without sacrificing the reaction rate is reported. The basic concept comprises the synthesis of a tertiary amine-functionalized polyrotaxane (PRX_NR1) accelerator: a molecular necklace structure that induces a high cross-linking density as well as active molecular movement. Fourier transform infrared spectroscopy and differential scanning calorimetry measurements confirmed that the PRX_NR1-containing epoxy resin afforded a high reaction rate. Furthermore, the cross-linking density and mechanical properties of the epoxy resin were confirmed by dynamic mechanical analysis and tensile testing. Consequently, the PRX_NR1-containing epoxy resin greatly increased the cross-linking density, thereby resulting in an increase in tensile strength and glass transition temperature. Interestingly, the epoxy resin exhibited a simultaneous increase in ductility which is important to avoid brittle fracture (low toughness) of the epoxy resins. These results indicate that the proposed molecular necklace-like supramolecular PRX_NR1 accelerator is highly effective to overcome the traditional drawbacks of an epoxy resin that pose significant problems in the industrial field.