The structure-properties relationships of native and debranched starch (DBS) were investigated by analyzing the results of DSC, XRD, NMR, HPAEC, FT-IR, SEM, hydrolysis, and digestibility properties. After debranching of starch in waxy rice, japonica rice, and indica rice, the linear short-chain molecules formed were easier to alignment and aggregation, and associate into a double helix. The crystalline structure of the rice starch after the pullulanase treatment was transformed from the type A to the type V crystalline by XRD measurement. Based on FT-IR and C-13 NMR observations, molecular rearrangement and degree of order in starch granules increased. The DSC curve showed an increase in gelatinization temperature of debranched starch compared to native starch. Meanwhile, Solubility, water holding capacity and resistant starch content of DBS also raised. The study of structure- properties relationship provides a theoretical foundation for the development of foods or drugs with targeted functional properties.