Pectin and flavonoids are important components of citrus fruits, but the effects of flavonoid grafting on the emulsifying properties of citrus pectin remain unclear. In this study, a novel natural citrus flavonoid-pectin conjugate in citrus peel was identified through alkaline hydrolysis combined with ultra-high performance liquid chromatography. Subsequently, two major citrus flavonoids were enzymatically conjugated to citrus pectin at high grafting rates (hesperidin: 20.21%; naringin dihydrochalcone: 16.11%). The flavonoids increased pectin amphipathy while ensuring a tighter conformation and denser network structure. These structural changes reduced the interfacial tension (from 20.6 to 18.4 mN/m) and increased the adsorbed layer thickness (from 11.8 to 37.8 nm), facilitating rapid pectin anchoring at the oil-water interface. These led to smaller droplet size and better emulsion stability. Prepared flavonoid-pectin conjugates with high grafting rates exhibited better emulsifying properties than those with medium grafting rates; hesperidin-pectin conjugates were more effective than naringin dihydrochalcone-pectin conjugates. The prepared flavonoid-pectin conjugates aid in the structural identification of natural flavonoid-pectin conjugates; they also facilitate analyses of the properties of these conjugates and offer new insights into improving the functional properties of pectins used in the food industry.