BACKGROUND Euryale ferox Salisb. is widely grown in China and Southeast Asia as a grain crop and medicinal plant. The composition, morphology, structure, physicochemical properties, thermal properties, and in vitro digestibility of North Euryale ferox seeds starch (NEFS), hybrid Euryale ferox seeds starch (HEFS), and South Euryale ferox seeds starch (SEFS) were studied. RESULT Of the varieties that were studied, the amylose content of NEFS (23.03%) was the highest. Starch granules of each variety were smooth, sharp, small, and had an average diameter of 2 μm. All three varieties were A‐type crystals with crystallinity ranging from 26.42% to 28.17%. The degree of double helix and the short‐range order ranged from 1.9006 to 2.5324 and 1.4294 to 1.6006, respectively. The high proportion of C1 region in NEFS (17.74%) and HEFS (17.66%) were found. Thermodynamic properties in North Euryale ferox seeds included the highest onset temperature (To) (71.43 °C), peak temperature (Tp) (76.60 °C), conclusion temperature (Tc) (82.77 °C), enthalpy of gelatinization (ΔH) (12.64 J g−1), and peak viscosity (1514 mPa·s). All three varieties maintained a low level of in vitro digestibility, with the highest resistant starch (RS) content (29.57%), the lowest rapidly digestible starch (RDS) content (27.07%), and the slowest hydrolysis kinetic constant (0.0303) in NEFS. CONCLUSION The results revealed that the low digestibility of NEFS was attributable to compact granules, high crystallinity, high degree of order, and strong thermal stability. These digestive, physicochemical, and thermodynamic properties provide information for the future application of Euryale ferox seed starch in the food industry. © 2022 Society of Chemical Industry.