Waterborne epoxy resin (WER) has excellent chemical stability, heat resistance, and mechanical properties, and its application in emulsified asphalt modification is receiving widespread attention in road maintenance. In this paper, the mechanical properties of waterborne epoxy resin modified emulsified asphalt (WEA) binder through different preparation processes were investigated, and the influence of WER on the microstructure, rheological properties, and low-temperature stability of emulsified asphalt was analyzed. The results show that WEA binders prepared using a two-step method can make the curing reaction of the modifier more complete and the mechanical properties more excellent. With the increase of modifier content, WER gradually formed a continuous skeleton structure in emulsified asphalt, and the critical content for the continuous phase of the system to transform from emulsified asphalt to WER was about 15 %. WER could undergo polymerization reactions in emulsified asphalt, and its modification process of emulsified asphalt was mainly physical modification. With the increase of modifier content, the linear viscoelasticity range of the WEA binder gradually decreased, and the high-temperature deformation resistance was significantly improved. The influence of loading frequency on rheological properties also gradually weakened. In addition, WER could significantly improve the high-temperature elastic recovery performance of emulsified asphalt. The elastic recovery rate of the WEA binder exceeded 98 % when the content of the modifier exceeded 15 %. However, WER had certain adverse effects on emulsified asphalt's low-temperature performance, so the modifiers' content should be strictly controlled.