The amylolytic action of α-amylase and amyloglucosidase has been implemented in the development of microporous cassava starches; however, the results have not been the best due to rigid and compact molecular packaging. The effect of hydrothermal processes and simultaneous enzymatic hydrolysis on the physicochemical, morphological and structural properties of cassava native starch was evaluated. Cassava native starch presented a rigid, smooth surface exempt of porosities, whereas treatment with annealing (ANN) caused a structural rearrangement during granular swelling, increasing the size and number of pores. The combined action of ANN followed by enzymatic modification (AME) augmented the processes of internal degradation (endo-corrosion) and pore widening (exo-corrosion), which improved the hydrophilic properties. Likewise, the dual treatment ANN + AME degraded the amorphous lamellae. Starch that was hydrothermally treated (ANN) and enzymatically modified for 24 h increased pore size; therefore, this is considered an effective method for the development of cassava-modified starches with porous-surfaces.