To address the deficiencies of traditional emulsified asphalt-pavement maintenance material in cohesive strength, high-temperature rutting resistance, as well as adhesion to aggregates, this study developed waterborne epoxy resin-modified emulsified asphalt (WEA) binders using a two-component waterborne epoxy resin (WER) and systematically investigated their modification mechanisms and pavement performance. The results indicated that WER emulsions and curing agents could polymerize to form epoxy resin within the emulsified asphalt dispersion medium, with the modification process dominated by physical interactions. When the WER content exceeded 12%, a continuous modifier network structure was established within the emulsified asphalt. The epoxy resin formed after curing could significantly increase the polarity component of the binder, thereby increasing the surface free energy. The linear viscoelastic range of the WEA binder exhibited a negative correlation with the dosage of the WER modifier. Notably, when the WER content exceeded 6%, the high-temperature stability (rutting resistance and elastic recovery performance) of the binder was significantly enhanced. Concurrently, stress sensitivity and frequency dependence gradually decrease, demonstrating superior thermomechanical stability. Furthermore, WER significantly enhanced the interfacial interaction and adhesion between the binder and aggregates. However, the incorporation of WER adversely affects the low-temperature cracking resistance of the binder, necessitating strict control over its dosage in practical applications.