This research investigates the properties and modification of water caltrop starch (WCS) with a particular focus on its potential for retrogradation and resistance to enzymatic hydrolysis. The study begins by obtaining WCS with a recovery efficiency of 4.5% (w/w in dry basis). The native WCS exhibits notable characteristics, including an apparent amylose content of 45.4%, a ratio of amorphous/α-helix regions at 1.341, a degree of relative crystallinity of 54.43%, an average molecular weight of 6.58×104 g/mole, and a degree of polymerization of 365.57. The high amylose content and degree of crystallinity in native WCS indicate its favorable retrogradation potential and resistance to enzymatic hydrolysis. Textural analysis of the WCS gel reveals high hardness and chewiness but low adhesiveness, which further supports its potential for retrogradation applications. To explore the effects of repeated retrogradation cycles, native WCS was subjected to 3, 6, and 9 cycles. The increase in retrogradation cycles led to a decrease in apparent amylose content from 31.79% to 29.34%. This reduction can be attributed to the formation of double helix associations and the emergence of new crystalline regions from amylose molecules. Furthermore, an increase in retrogradation cycles resulted in enhanced syneresis of starch. Interestingly, as the number of retrogradation cycles increased, the enzymatic hydrolysis rate of retrograded WCS gradually decreased. Correspondingly, the estimated glycemic index (GI) of the samples decreased, reaching a range of 50.05 to 38.46. Consequently, treatment with repeated retrogradation proves to be an effective strategy for producing modified WCS with a low glycemic index (<50%), thereby presenting promising opportunities for low glycemic index applications.