Waterborne epoxy resin (WER), a cleaning material with exceptional high-temperature resistance, has attracted much attention to modify emulsified asphalt in the pavement material field. Epoxy value is the critical characteristic index of WER. In this research, three WER with the epoxy values of 0.20 eq/100g, 0.44 eq/100g, and 0.51 eq/100g were utilized as asphalt modifiers. The influence of epoxy value on WER-EA was investigated by comparing the rheological properties of three kinds of WER emulsified asphalt (WER-EA). The modification mechanism of WER-EA has been analyzed using FTIR and SEM. The results demonstrate that different WER-EA resulted in significantly different rheological properties. WER-EA with the epoxy value of 0.20 eq/100g (E20) performed best at high temperatures, with a maximum increase of 17477% in G*/sinδ compared to the neat asphalt and a maximum increase of 66.3% in G*/sinδ compared to the other two WER-EA. WER-EA with 0.44 eq/100g epoxy value (E44) performed best at low temperatures, with a maximum increase in m value of 39.4% and a maximum decrease in S value of 33.3% compared to the other two WER-EA. In addition, the interpenetrating polymer network (IPN) in E20 was observed to be more solid and stable, and IPN in E44 was more uniform. To summarize, lower epoxy value led to a higher degree of WER reaction and higher content of rigid groups, which is more conducive to optimizing the high-temperature property of WER-EA. WER with moderate epoxy value resulted in a low content of polar bonds and thus high content of flexible segments, which helps emulsified asphalt to form a more uniform IPN.