Current researches in the pavement engineering field are neglecting the influence of the chemical structure of curing agents on rheological properties of waterborne epoxy resin (WER) emulsified asphalt. The length of molecular chain and the number of active groups will affect the rigidity and flexibility of WER emulsified asphalt. In this study, three curing agents (TETA\DETA\593) with obvious differences in molecular chain length and number of active groups were selected to modify emulsified asphalt. The three kinds of WER emulsified asphalt were subjected to the conventional properties, DSR, BBR, SEM and FITR test. The research has found that the addition of WER system makes emulsified asphalt produce three-dimensional network structure, which significantly improves the high-temperature performance and temperature sensitivity of emulsified asphalt. Whereas, the low-temperature performance of WER emulsified asphalt deteriorates. This indicates that the high-performance of WER emulsified makes it more suitable for the adhesive of micro surfacing or cold mix asphalt used in heavy-load traffic in medium and high temperature areas. Curing agent TETA has the greatest impact on WER emulsified asphalt at high-temperature while 593 has the least adverse influence on the low-temperature performance. The results demonstrate that the more active groups in the curing agent, the higher the crosslinking degree and complexity of the three-dimensional network structure in WER emulsified. And it will lead to the better high-temperature performance of WER emulsified. The longer the molecular chain of curing agent, the more flexible chains in WER emulsified. And it will lead to better flexibility of WER emulsified.