Existing research shows that using waterborne epoxy resin (WER) instead of emulsified asphalt as the binder for cold mix asphalt (CMA) can enhance the rutting resistance, high-temperature performance, fracture performance, and early performance of CMA. In order to eliminate the potential drawbacks such as insufficient strength and low-temperature performance of CMA during application, a novel method was proposed in this study for the preparation of waterborne epoxy-acrylate resin (WER), specifically tailored to modify emulsified asphalt, resulting in waterborne epoxy-acrylate resin emulsified asphalt (WEREA). The modification effect of WER on emulsified asphalt was evaluated through rheological tests and direct tensile tests. A modified design method based on the conventional Marshall design method was proposed to determine the optimal mix proportions, including the key parameters of specimen compaction and curing. The results revealed that the incorporation of WER led to a substantial improvement in the complex shear modulus and a concurrent decrease in the phase angle. When the temperature exceeded 60 °C, the phase angle exhibited a diminishing trend, indicative of a reduced viscosity as temperatures escalated. As the WER content increased, a decrease in the direct tensile strain rate was observed, accompanied by a substantial elevation in direct tensile strength. At various stress levels, the shear strain of WEREA decreases with increased content of WER, indicating that the incorporation of WER can enhance the hardness of emulsified asphalt and improve its deformation resistance. The results from MSCR tests indicate that WER could significantly improve the elasticity and hardness of emulsified asphalt, transitioning it from a viscoelastic material to an elastic material, thereby improving its deformation resistance, resistance to rutting, and high-temperature performance. The results of fatigue life are consistent with those of the amplitude sweep, both reflecting the improvement of resistance to deformation of emulsified asphalt by WER. This indicates that WER has a significant improving effect on the fatigue resistance of emulsified asphalt. Furthermore, the Marshall design tests further confirmed the advantages of WEREA in asphalt mixtures. The optimal preparation for the WEREA mixture was proposed as follows: double-sided compaction for 50 times each, aging at 60 °C for 48 h, optimal moisture content of 5.14%, cement content of 2.5%, and emulsion content of 8.4%. The optimal mix proportions identified through these tests yielded asphalt mixtures with significantly improved stability, reduced flow value, and enhanced rutting resistance compared to the hot-mix asphalt mixture (HMA) of AC-16. These findings suggest that WEREA has the potential to significantly enhance the durability and longevity of asphalt pavements. For future applications, it can be explored for use in producing cold recycled asphalt mixtures. In addition to designing the WEREA mixture according to AC-16 gradation, consideration can also be given to using a gradation with a smaller nominal maximum aggregate size for the application in the surface layer or ultra-thin wearing course.