Starch digestion in pulse cellular matrices is primarily determined by the hindrance of cell walls limiting enzyme diffusion as well as the retention of starch granular structure. However, the effect of hydrothermal treatment on structure and digestion properties of entrapped pulse starches is not fully elucidated. In present study, we reported the variations in structure and enzyme susceptibility of pulse cells isolated at 60 °C followed by heated at 70, 80, 90, 100 °C, which were higher than the starch gelatinization temperature. Based on the thermal and crystalline properties, entrapped starches in pulse cells were not fully gelatinized even treated at 100 °C. Whilst, the digestion of entrapped pulse starches increased with higher temperature, but still much lower than the isolated starch treated at the same temperature. In addition to physical barriers (intact cell wall) and starch structural features (partial ordered crystalline structure), the soluble/insoluble proteinaceous materials in cells also synergistically reduced the starch digestibility.