A method for efficient functional modification of starch granules by thermal ethanol pre-treatment and subsequent maltogenic α-amylase (MA) and branching enzyme (BE) post-treatments is described. Ethanol pre-treatment significantly increased the swelling power of starch granules thereby increasing the MA and BE susceptibility. Ethanol pre-treated granules became shrunk and twisted after incubating in buffer. Sequential MA post-treatments remarkably increased the α-1,6 to α-1,4 ratio and the content of amylopectin short chains (DP 1–10), contributing to the low retrogradation rate. BE post-treatments significantly decreased the product yield, increased the relative crystallinity of starch granules, suggesting BE had intramolecular transglucosylation activity which altered the branch position and reduced the molecular size by forming cyclic structures. Moreover, BE post-treatments showed an α-1,6 to α-1,4 transglucosylation activity by decreasing the α-1,6 to α-1,4 ratio, especially during simultaneous MA and BE catalysis. However, in the simultaneous MA and BE post-catalysis, MA dosage was predominant by noticeably hydrolyzing amylopectin and amylose molecules and increasing the α-1,6 to α-1,4 ratio, thereby leading to the lowest digestibility and retrogradation.