Abstract: This study investigated the interaction between pectin and cyanidin-3-glucoside (C3G), as well as its impact on the gastrointestinal stability of C3G, using high-ester and low-ester pectin from different sources. Experimental results on aggregation and binding behavior indicated that low-ester pectin was less prone to aggregate formation and contained abundant free carboxyl groups, primarily binding to C3G through strong electrostatic interactions. The binding rate of C3G with low-ester pectin was significantly higher than that of high-ester pectin, which relied predominantly on hydrogen bonds. Among the samples, low-ester citrus pectin exhibited the highest binding rate, reaching 66.80%. Physicochemical analysis revealed that low-ester pectin formed a composite with C3G characterized by smaller particle size, more negative zeta potential, and a denser, more uniform structure, with C3G effectively encapsulated within the pectin network. In contrast, high-ester pectin primarily formed loose aggregates by adsorbing C3G onto its surface. In vitro gastrointestinal digestion simulations revealed that the low-ester pectin-C3G complex exhibited high stability. After intestinal digestion, the total C3G content in low-ester citrus pectin-C3G group increased by 65.58% compared to the control group, significantly enhancing the gastrointestinal stability of C3G. In summary, low-ester pectin improves the gastrointestinal stability of C3G more effectively by binding and encapsulating it within the aggregated pectin structure through electrostatic interactions.