The effects of heat‐moisture treatment on structure and properties of big Coix seed (BCS), translucent Coix seed (TCS), and small Coix seed (SCS) starches were investigated in this study. The amylose contents of BCS, TCS, and SCS starches were 0.63, 24.12, and 0.96%, respectively. After HMT, starches appeared cracks and broken, birefringence weakened and the relative crystallinity and the ratio of 1047 cm−1/1022 cm−1 of HMT starches decreased, owing to disorganization of double helices and disruption of crystalline regions. The gelatinization temperatures of HMT starches increased but the thermal enthalpies decreased. The rheological characteristics had been changed, and HMT starches had the better flowability, especially for TCS starch. HMT increased rapidly digestible starch and resistant starch (RS) levels, and decreased slowly digestible starch levels. The TCS starch had the highest RS content (70.36%). The results show that the HMT has significant impacts on the structural and physicochemical properties of different varieties Coix seed starches but to different extents.