To improve the pavement performance of emulsified asphalt (EA) and reveal the compound modification mechanism of waterborne epoxy resin and styrene butadiene rubber latex (WER/SBR) to EA, the EA samples with different WER/SBR dosages were first prepared. Then the influences of WER/SBR on the basic properties, rheological performance, low-temperature cracking resistance, thermal stability, chemical compositions, phase microstructure, and micromorphology of evaporation residues of EA were discussed using basic property tests, dynamic shear rheometer (DSR) test, bending beam rheometer (BBR) test, Fourier transform infrared spectroscope (FTIR) test, differential scanning calorimetry (DSC) test, X-ray diffraction (XRD) test, laser scanning confocal microscope (LSCM) test and environmental scanning electron microscope (ESEM) test. Results show that the penetration, softening point, and ductility of EA were improved by SBR, but the ductility was decreased by WER. SBR formed a network film through the physical action, enhancing the toughness of EA. WER formed a high-strength network through the chemical reaction, improving the high-temperature thermal stability of EA. However, the low-temperature cracking resistance of EA is deteriorated with the increase in WER dosage. Additionally, when the WER dosage was lower, the WER particles as dispersed phase exist in the asphalt continuous phase, and the SBR network film shows a strong cross-linking degree. When the WER dosage is 6%, the SBR network film is damaged to a certain extent. Also, the high-strength network formed by WER and the unbroken SBR network are interpenetrated to form a more compact and stable three-dimensional network. Meanwhile, the interlayer spacing and crystallite size of EA reach the maximum values. When the WER dosage is 8%, the three-dimensional network is damaged, and the compatibility between WER and asphalt becomes unsatisfactory. Finally, the WER dosage of 6% is proposed to combine with SBR dosage of 3% for preparing WER/SBR modified EA.