The effects of treatment time of continuous annealing (ANN) and cycle numbers of cycled ANN on the structural, physicochemical, and digestive properties of water caltrop starch were studied under 70% moisture at 65 °C. It was found that continuous and cycled ANN have no significant effects on the morphology of starch granules. However, the relative crystallinity and content of resistant starch increased pronouncedly, possibly due to crystalline perfection, which also led to the rise in gelatinization temperature and the narrowed gelatinization temperature range of starch. The treatment time in continuous ANN generally showed a pronounced effect on the rheological properties of water caltrop starch. During pasting, the breakdown viscosity and setback viscosity of all treatment decreased, implying that ANN modified starch was less susceptible to the condition in heating and continuous shearing, and less likely to cause short-term retrogradation. In contrast, peak viscosity decreased with increasing treatment time of continuous ANN, indicating crystalline perfection restricted the swelling of starch granules and viscosity development during pasting process, which was consistent with the results of steady and dynamic rheological evaluation. All ANN-modified samples showed pseudoplastic behavior with weak gel viscoelastic characteristic. Under a total annealing time of 96 h, the pasting and rheological properties of water caltrop starch were essentially less affected by annealing cycle numbers. However, multistage ANN showed stronger resistance to enzyme hydrolysis.