In this paper, a novel modified epoxy resin with an interpenetrating network structure for use as a grouting material with high toughness was prepared by a method of graft copolymerization between polyurethane prepolymer (PUP) trimer and epoxy resin (E-44). Polyurethane prepolymer was synthesized using poly(propylene glycol) (PPG) and 2,4-toluene diisocyanate trimer (TDIT) at 70 °C for 3 h. The graft copolymer was prepared by grafting polyurethane prepolymer onto the side chain of epoxy resin at 110 °C. The mechanical properties, fracture surface morphology, chemical structure, thermal properties, and corrosion resistance of the modified epoxy resin curing products were studied. Due to the beneficial flexible segments and the interpenetrating network structure, the results show that when the ratio of epoxy resin to polyurethane prepolymer is 10:2, the optimum mechanical properties are obtained; these include a compressive resistance of 184.8 MPa, impact property of 76.6 kJ/m², and elongation at break of 31.5%. At the same time, the modified epoxy resin curing product also has excellent heat and corrosion resistance. This work provides a new method for the study of epoxy resins with high performance.