Neat asphalt emulsions have poor physicochemical properties. In order to endow neat asphalt emulsions with excellent physicochemical properties and broaden their application as pavement, this study adopted the composite modification method using waterborne epoxy resin (WER) and styrene–butadiene rubber (SBR) latex. Firstly, a waterborne-epoxy–SBR composite modified asphalt emulsions (WESAEs) with different amounts of WER were prepared, and the storage stability, workability, and residual properties were characterized with a series of tests. Then, the performance of the WESAEs was comprehensively evaluated by multiobjective gray target decision-making method, through which the optimal amount of WER in WESAE was determined. Lastly, the modification mechanism of WER was revealed by Fourier-transform infrared spectroscopy test. The results show that the incorporation of WER improves the high-temperature performance, thermal stability, rheological property, and adhesion of the SBR modified asphalt emulsion (SBRAE) residues. However, an excessive amount of WER will adversely affect the storage stability, particle distribution uniformity, and workability of the WESAE binder. The WESAE with 3% WER showed the best comprehensive performance; thus, the optimal amount of WER is 3% of the weight of the WESAE. Additionally, modification of the SBRAE by WER is a physical blending process, meaning no chemical reaction occurs in the blending process.