Quinoa starch granular structure as affected by nonenyl succinic anhydride (NSA) substitution was investigated by multiple approaches, including scattering, spectroscopic, and microscopic techniques. The modification had little impact on the morphology of starch granules. The NSA substitution was found mainly in the amorphous lamellae and amorphous growth rings. The NSA modification increased the thickness of the amorphous lamellae. The homogeneity of the ordered structure in the granules was improved, probably because the NSA modification reduced the amount of defects in the semi-crystalline growth ring. Compared to other chemical modifications such as acylation, succinylation was more effective in modifying the starch lamellar structure. A possible reaction pattern of NSA modification on quinoa starch is proposed, in which the NSA modification may follow the sequence of amorphous growth rings, the amorphous matrices among blocklets, amorphous and crystalline lamellae in semi-crystalline growth rings. This study provides new insights on the structural changes of starch granules induced by succinylation on the supramolecular level.