In this study, the cyanidin-3-O-glucoside (C3G)-binding capacities of three native starches were investigated. While potato starch had the largest binding capacity of 0.34 mg/100 mg, corn and pea starch had binding capacities of 0.17 and 0.06 mg/100 mg. Confocal microscopy confirmed the binding results and revealed close associations between the surface properties and binding capacities. These findings were further substantiated with wettability and gelatinization results. The morphological observations showed that corn starch had advantageous particle sizes and more surface gullies, providing more opportunities to bind C3G. The zeta potential results, however, indicated that potato starch had the highest negative surface charges (−24 mV). These favorable electronic characteristics were believed to be responsible for the strongest electrostatic interactions. Hydrogen bonds, however, had a negligible effect on the formation of complexes. Overall, the negative surface charges and specific surface areas of the native starches were the most important factors determining C3G-binding capacities.