The functional properties of starch-polyphenol complexes closely related to the digestion process. Here, dynamic in vitro digestion properties and prebiotic activities of lotus seed starch-chlorogenic acid complexes under autoclaving treatment (A-LS-CA) were investigated. The results showed that the ordered structure, thermal stability and molecular weight of the A-LS-CA complexes significantly altered during dynamic in vitro digestion. Remarkably, the ordered structure of digestive products significantly decreased in oral-gastric phase, while the ordered structure was increased in oral-gastric-small intestinal phase. The molecular weight of A-LS-CA complexes decreased gradually in oral, oral-gastric and oral-gastric-small intestinal phase, which were 7.40 +/- 0.57, 2.23 +/- 0.98 and 0.46 +/- 0.10 x 107 g/mol, respectively. In addition, chlorogenic acid was attached to the surface of starch by hydrogen bonding during dynamic in vitro digestion, improving the bioavailability of chlorogenic acid. Interestingly, the dynamically digested A-LS-CA complexes stimulated the proliferation of Bifidobacterium longum subsp. infantis, Bifidobacterium adolescentis, Lacticaseibacillus rhamnosus and Lacticaseibacillus casei, and promoted to produce acetic acid, which was 1.07-1.49 folds that of the controls. In summary, this study provided a new insight for the structural and functional properties of starch-polyphenol complexes.