In research aimed at improving the brittleness of WER (waterborne epoxy)-modified emulsified asphalt, commonly encountered issues are that the low-temperature performance of this type of asphalt becomes insufficient and the long curing time leads to low early strength. Matrix-emulsified asphalt was modified with WPU (waterborne polyurethane), WER, and DMP-30 (accelerator). Firstly, the performance changes of modified emulsified asphalt at different single-factor dosages were explored through conventional performance tests and assessments of its adhesion, tensile properties, and curing time. Secondly, based on a response surface methodology test design, the material composition of the composite-modified emulsified asphalt was optimized, and its rheological properties were analyzed by a DSR test and a force–ductility test. Finally, the modification mechanism was explored by scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR). The results show that WER can improve the adhesion strength of modified emulsified asphalt and greatly reduce elongation at break. WPU can effectively improve the elongation at break of composite-modified emulsified asphalt, but it has a negative impact on adhesion strength. DMP-30 mainly affects the curing time of modified emulsified asphalt; EPD (composite modification) can effectively improve the high-temperature rutting resistance of matrix-emulsified asphalt, and its low-temperature performance is significantly improved compared with WER-modified emulsified asphalt. The EPD modification process mainly consists of physical blending. In the case of increasing the curing rate, it is recommended that the contents of WER and WPU be lower than 10% and 6%, respectively, to achieve excellent comprehensive performance of the composite modification.