Due to the issue of weakened adhesion between ultra-thin surface overlays, higher demands have been placed on bonding layer materials in practical engineering. This study proposed a method for preparing a one-component waterborne epoxy resin-modified emulsified asphalt (OWEEA) and explored the impact of different ratios on its performance. The basic physical and mechanical properties of the OWEEA, as well as its rheological characteristics, were investigated through penetration tests, softening point tests, ductility tests, tensile tests, and dynamic shear rheological tests. Pull-out tests and shear tests considering different substrates were used to evaluate the interfacial bonding performance of the OWEEA as a bonding layer material, and comparative analysis was conducted with conventional waterborne epoxy resin-modified emulsified asphalt. Based on microscopic testing and analysis, the laws of physical and chemical changes and secondary curing characteristics of the one-component waterborne epoxy emulsion (OWE) during the modification of emulsified asphalt were elucidated. The results indicated that the OWE prepared in this study significantly enhanced the tensile strength and bonding properties of emulsified asphalt. The results showed that the tensile strength, bonding strength, and shear strength of the OWEEA increased from 0.15 MPa, 0.36 MPa, and 0.35 MPa to 0.55 MPa, 1.29 MPa, and 2.01 MPa, respectively. The modification effect of the OWEEA surpassed that of conventional waterborne epoxy emulsion, albeit with a certain reduction in elongation at break, reduced from 1551% to 98%. Furthermore, the OWEEA showed a distinct secondary curing phenomenon. The results of the SEM tests showed that high temperatures accelerated the formation of the crosslinked network structure of OWE, promoting its integration with emulsified asphalt and resulting in a more uniform and dense structure, significantly enhancing bonding strength in a short period. In the actual road construction process, laying hot-mix asphalt mixtures on the bonding layer can further enhance its curing effect and improve its bonding performance.