Water caltrop has a high starch content and is a promising resource of starch in Asia. Starch can be divided into rapidly digestible starch (RDS), slowly digestible starch (SDS), and resistant starch (RS). Here, the effects of physical modification by microwave treatments, heat–moisture treatments, and pressure–heat treatments on the physiochemical and structural properties and on the in vitro digestibility of water caltrop starch is studied. The results show that, compared with native starch (NS), the solubility and swelling power of modified starch samples decrease with prolonged microwave and heat–moisture treatment. The infrared absorbance ratio at 1047 cm−1/1022 cm−1 is decreased in starch samples modified by microwave treatment and pressure–heat treatment, the NS samples present a C‐type crystalline pattern which changes into an A‐type pattern upon microwave treatment. Water caltrop starch subjected to 50 s of microwave treatment has the highest amylose (48.78%), the highest crystallinity (42.95%), and the highest RS content (67.41%, uncooked and 48.91%, cooked). Water caltrop starch subjected to 3 h of heat–moisture treatment contains the highest SDS content (54.33%, uncooked and 60.11%, cooked).