Emulsified asphalt mixtures’ cold mix and paving features facilitate asphalt pavements in fulfilling dual-carbon and energy-saving demands. Anionic emulsifiers can enhance emulsion stability, ensure uniform dispersion of oil and water, possess good decompression viscosity, thickening, and lubricating properties, and maintain good stability under acidic conditions. Nevertheless, anionic emulsified asphalt is restricted in engineering applications due to problems like its storage stability. In this paper, eight anionic emulsifiers and two preparation procedures were chosen for stability tests. Through static tests, storage tests, sieve residue tests, and laser particle size tests, the impacts of emulsifiers on the storage stability and dispersion of asphalt were analyzed. Waterborne epoxy resin exhibits excellent adhesive properties, mechanical properties, chemical resistance, and heat stability. A fluorescence microscope test, static and storage test, laser particle size test, and cementation test were employed to explore the effects of different preparation processes and waterborne epoxy mixing ratios on emulsified asphalt’s storage stability, dispersion stability, and structural stability. The results showed that: (1) the emulsified asphalt prepared with the BWH-02 emulsifier exhibits the best storage stability, and blending with 20% of the waterborne epoxy modifier can notably enhance the bonding properties; (2) the shear strength of the BWH-02 waterborne epoxy emulsified asphalt prepared can reach 1.543 MPa, and the tensile viscosity can reach 0.848 MPa; (3), The emulsified asphalt prepared by the process of modification has better storage stability than that prepared by the side of the emulsification process. Moreover, the storage stability of emulsified asphalt prepared by emulsification and modification is superior to that of the emulsification and modification process. This research provides theoretical and technical support for popularizing and applying cold-mixed cold-paving asphalt mixtures.