In order to solve the problems of poor temperature sensitivity, low mechanical strength, and poor pavement performance of traditional emulsified asphalt pothole repair materials, two-component waterborne epoxy resin (WER) was used to modify emulsified asphalt in this research. The influence of the WER modifier on the pavement performance of emulsified asphalt binder and its mixture was studied. The research showed that WER emulsion and curing agents could polymerize and produce epoxy resin under the condition of emulsified asphalt as the dispersion medium. Fourier transform infrared spectra analysis indicated that the modification process of emulsified asphalt by WER was mainly physical modification. With the increase of WER content, the mechanical properties and high-temperature deformation resistance of waterborne epoxy resin modified emulsified asphalt (WEA) binder were significantly improved. The mechanical properties of the WEA mixture had an excellent linear correlation with the water loss rate. When the WER content exceeded 15%, the mechanical properties, water stability, high-temperature stability, and anti-stripping performance of the WEA mixture were significantly improved. When the WER content was less than 20%, the modifier played a reinforcing role in the emulsified asphalt binder, and the low-temperature crack resistance of the WEA mixture gradually improved with the increase of the modifier content. After exceeding the critical content, the WEA mixture gradually exhibited brittleness and hardness, and its low-temperature performance decreased. In summary, it was recommended that the content range of the WER modifier be 15-20% for the pothole repair material system in this research.