Since starch is a native biomaterial for anthocyanin delivery, its binding capacity plays a crucial role in its applications. In this study, four starch fractions derived form starch (granule, outer shell, blocklet, molecules including AM and AP) were separated and characterized. Following that, their interactions with cyanidin-3-O-glucoside (C3G) under different pH conditions (3, 5, and 7) were investigated. The structural characteristics of outer shell appeared to increase its binding capacity. It was found that outer shell exhibited the highest binding capacity to C3G at pH 3, resulting in enhanced oxidation, photolysis, and simulated in vitro digestion stability. To explain the highest binding capacity of outer shell, interactions between each starch biomaterial and C3G was revealed through microscopic morphology, ordered structure, and interaction force. It was observed that C3G disrupted the morphology and ordered structures of starch biomaterials through bridging interactions. Additionally, electrostatic interactions played a dominant role in the binding of outer shell/granule with C3G, while hydrogen bonds were primarily involved in the binding of blocklet/AM/AP with C3G. In summary, C3G exhibited strong electrostatic interactions with both the exterior and interior of the outer shell, owing to its large spatial structure, which contributed to the enhanced binding capacity and stability of C3G.