The effect of branched limited dextrin (BLD) on starch retrogradation was investigated to explain the anti-firming mechanism of α-amylase. The influence of BLD on the gelatinized wheat and waxy rice starch retrogradation was characterized by differential scanning calorimetry (DSC) and wide-angle X-ray diffraction (WXRD). DSC and WXRD results showed that retrogradation of wheat and waxy rice starch gels were reduced with the addition of branched limit dextrins (F75 and F88). Avrami equation was used to analyze the enthalpies of retrograde wheat starch gels, and the value of k indicated that F75 and F88 reduced the kinetics of starch retrogradation. In addition, molecular dynamic (MD) simulation was adapted to predict the interaction of BLD and starch fraction, and the results showed that the BLD reduced starch retrogradation by the interplay between starch and BLD.