Good compatibility between waterborne epoxy resin (WER) modifier and styrene-butadiene rubber (SBR) latex modified asphalt emulsion (SBRE) is an essential premise for good pavement performance of WER and SBR latex compositely modified asphalt emulsion (WSAE). This study aims to explore the compatibility between WER modifier and SBRE. To achieve the goal, several WER modifiers produced by two methods were first selected to modify SBRE, thus the WSAEs were prepared. Next, storage stability and workability of the WSAEs themselves, and high-temperature performance, rheological behavior and temperature sensitivity of their evaporated residues were compared and evaluated via performing a series of experiments, respectively, thus the WER modifier possessing an optimal modification effect was recommended. Results show that the storage stability of WSAEs is sensitive to the amount of WERs. The incorporation of 1% WERs by the mass of SBRE improves the storage stability of SBRE, while WERs that exceed 1% weaken its storage stability. When the WERs reach 3% and 4%, the 5 d storage stability of prepared WSAEs will be beyond the limitation of specification. Incorporating WERs into SBRE negatively affects the workability of SBRE, and the workability of WSAEs is adversely influenced by the WERs content and the storage time. To ensure the construction, the WSAEs with 3% and 4% WERs should not be stored for more than 36 h and 48 h, respectively. The WERs effectively improve the high-temperature performance of SBRE residue, especially the 3% WERs. Besides, the WERs notably enhance the rheological property and thermal stability of SBRE residue. In contrast, the WER modifier produced by chemically modified method has a smaller adverse impact on the storage stability and workability of WSAE, and a larger enhancement on the high-temperature performance, rheological property and thermal stability of SBRE residue, which is thus recommended to modify SBRE. •The workability of WSAEs is associated with the WERs dosage and the storage time.•WERs enhance the high-temperature, rheological and temperature-sensitive properties of SBRE residue.•The chemically-produced WERs exhibit a superior modification effect.