Cold-mixed asphalt mixture is a widely recommended asphalt pavement materials with potentially economic and environmental benefits. Due to the reduction of natural non-renewable mineral resources, powder minerals with similar properties are considered as new mineral fillers in asphalt mixtures. This study explored the feasibility of using cement to replace natural limestone powder (LP) in emulsified asphalt concrete modified by styrene-butadiene styrene copolymer. The experimental tests, including compressive strength, Marshall stability as well as moisture susceptibility test, were used to investigate the mechanical properties, the Marshall stability, flow value, as well as the moisture damage. In addition, the influence of material composition on the performance of asphalt concrete is explained by the microstructure evolution of the pore structure, the interface transition zone (ITZ), and the micromorphology. Due to mineralogical reactivity of cement, its replacement part of LP improved the mechanical properties, Marshall stability, but it will reduce the moisture susceptibility and flow value. This is because with the increase of the cement substitution rate, the pore structure of the asphalt concrete is refined, the width of ITZ becomes smaller, and the microstructure is more compact. In addition, asphalt concrete with a larger nominal particle size (AC-16) has relatively better performance.