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Starch-based materials with reinforced properties were considered as one of the most promising materials to replace the petro-based packaging products, and actually, the molecular structures of starch usually determined the structures and properties of end-used starchy products. Here, starch-based nanocomposites were fabricated by starch esters derived from native starches with different amylose contents and organically modified montmorillonite (OMMT). The fractured surface under scanning electron microscopy (SEM) exhibited wrinkles formed by macromolecular aggregation owing to the interaction competition between the plasticizer and nanofiller with the starch ester. The more intense interaction within amylopectin-rich films promoted the formation of much randomly exfoliation of OMMT observed by Transmission electron microscopy (TEM). As the amylose content increased, the interaction between the starch ester and the nanofiller was weakened, leading to the dispersion morphology of an ordered arrangement and partly intercalated structures in the dimension of 12.92 to 19.77 nm. Meanwhile, such interaction also affected both the inner ordered structure integrity of starch ester and the layer structure consistency of nanofiller according to X-ray diffraction results. Further, the stronger interaction between amylopectin and the nanofiller endowed higher thermal stability to the amylopectin-rich starch-based nanocomposites. In short, these results are beneficial for the application of starch-based nanocomposites in the food packaging industry by regulating the interaction between starch and nanofillers.