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Using combined analytical techniques (SEM, synchrotron-SAXS, XRD, DSC, FTIR, etc.), this work provides insights into how the structural heterogeneity on multiple length scales affects the digestion of granular amylopectin. Native amylopectin displayed a dual-phase digestion behavior, as the heterogeneous supramolecular structure of amylopectin endowed the starch molecules with different enzymatic susceptibilities. Alkali disrupted the amorphous matrix, as well as partial growth rings, blocklets, lamellae and crystallites, resulting in weakened amylopectin molecular packing and thus enhanced susceptibility of amylopectin molecular chains to a-amylase molecules. In particular, the stronger alkali (0.5% w/w) more prominently increased the multi-scale structural heterogeneity and even transformed the dual-phase digestion of amylopectin into a triple-phase pattern. These results confirms that the structural heterogeneity of amylopectin predominantly governs its enzymatic digestion, and treatments such as alkali may serve as simple methods to modulate starch supramolecular structural heterogeneity and thus to rationally develop starch-based foods with desired digestibility.