To investigate the potential of modified epoxy resin for repairing and strengthening historical wooden structures, this study utilized polyurethane and silicone-modified epoxy resin as the base, alongside a polyamine curing agent. The resin mixture was cured at ambient temperature, resulting in the creation of ten unique epoxy resin systems. Investigation into the chemical structure and alterations to the glass transition temperature were conducted. The study conducted tests and characterization of viscosity, curing rate, mechanical properties, stress failure mode, hygrothermal aging resistance, and bonding properties. The results reveal that the curing degree of the two modified epoxy resins is high after being cured at room temperature, and the chemical structure and curing rate show insignificant changes. The range of the glass transition temperature for the modified epoxy resin is between 61.31 °C and 70.51 °C. The incorporation of polyurethane and silicone molecular chains into the epoxy resin cross-linking curing system enhances the toughness of the epoxy resin. The modified resin achieves a maximum elongation at break that is 5.18 times greater than that of the unmodified resin, along with a maximum tensile strength and a compressive strength that are 7.94 and 1.74 times, respectively, higher than those in the Chinese technical specifications for the maintenance and reinforcement of ancient wooden structures. The increase in toughness changes the failure mode of the cured epoxy resin. The modified epoxy resin exhibits great bonding ability to aged wood, with a shear strength of up to 9.6 MPa along the grain. As a result, the modified epoxy resin meets the requirements for the reinforcement and repair of the timber members of ancient buildings.