The addition of amino acids (AAs) including glycine (Gly), lysine (Lys) and glutamic acid (Glu) with different concentrations on starch morphological, physicochemical and in vitro digestion properties were studied. While AAs showed no effects on neither morphology nor crystalline characters, they all significantly influenced the starch relative crystallinity and swelling capacity in an order of Glu > Lys > Gly. For all samples, both fastly- and slowly- digestible starch fractions (SF and SS) were observed. While Glu and Gly increased SF content with a faster digestion rate, they reduced SS content with a slower digestion rate. On contrary, Lys reduced SF content and the digestion rate of SS. The inhibitory effects of AAs on starch retrogradation and enzyme activities, the acidic environment and Maillard reaction between starch phosphate monoester and Lys are responsible for altered starch digestibility. This study betters our understanding concerning how AAs interactions affect starch functional properties.