The influence of hydrothermal treatments on the structural properties and digestibility of water caltrop starch was investigated. Scanning electron microscopy (SEM) showed some small dents on the surface of starch granules for samples treated with heat moisture treatment (HMT), but not for samples treated with annealing (ANN) which generally showed smoother surfaces. The gelatinization temperature of starch was generally increased by hydrothermal treatments, accompanied by a trend of decreasing breakdown viscosity. These results implied the improvement of thermal and shearing stability, particularly for HMT in comparison to ANN. After being cooked, the native and ANN-modified water caltrop starch granules were essentially burst or destroyed. On the other hand, the margin of starch granules modified by HMT and dual hydrothermal treatments remained clear with some channels inside the starch granules. X-ray diffraction revealed that the crystalline pattern of water caltrop starch changed from the C -type to the A-type and the relative crystallinity reduced with increasing moisture levels of HMT. Results of ANN-modified water caltrop starch were mostly similar to those of the native one. Moreover, water caltrop starch modified with HMT20 and dual modification contained a pronouncedly higher resistant starch content. These results suggested that HMT, ANN, and dual modification effectively modified the functional properties of water caltrop starch.