Structural transformation of crystallized debranched cassava starch prepared by temperature cycling (TC) treatment and then subjected to annealing (ANN), heat-moisture treatment (HMT) and dual hydrothermal treatments of ANN and HMT was investigated. The relative crystallinity, lateral crystal size, melting temperature and resistant starch (RS) content increased for all hydrothermally treated samples, but the slowly digestible starch (SDS) content decreased. The RS content followed the order: HMT → ANN > HMT > ANN → HMT > ANN > TC, respectively. The HMT → ANN sample showed a larger lateral crystal size with more homogeneity, whereas the ANN → HMT sample had a smaller lateral crystal size with a higher melting temperature. After cooking at 50% moisture, the increased RS content of samples was observed, particularly for the ANN → HMT sample. These results suggest that structural changes of crystallized debranched starch during hydrothermal treatments depend on initial crystalline characteristics and treatment sequences, influencing thermal stability, enzyme digestibility, and cooking stability.