High amylose starch shows wide applications in food and non-food-based industries. Traditional complex-precipitation approach for the amylose fractionation required a large volume of organic reagents and was possibly risky for food safety. The object of this work was to establish a novel method to obtain starch fractions rich in amylose from debranch starch through repeated short-term retrogradation and centrifugation. Four starch fractions were obtained with the amylose content of 52.08% (C1), 62.28% (C2), 63.58% (C3), and 64.74% (C4). The thermograms of samples displayed that multiple endothermic peaks were detected in C1 and C2 and only one endothermic peak with melting temperature over 120 °C were observed in C3 and C4, indicating their differences in retrogradation behavior. The chain length distribution results of sample exhibited that C1 and C2 contained more short chains (DP ≤ 24), while C3 and C4 consisted of mainly long chains (DP ≥ 25). Accordingly, the differences in fine structures could provide more choices for these fractionated high amylose starch to utilize in practical applications.