Three-dimensional polymeric network of hydrogels avoids its dissolution into the aqueous region. Hydrogels must have strong structural integrity to be used for drug/nutraceutical delivery. A three factor-three-level Box-Behnken design was used to understand the effects of starch concentration, NaCl, and pH on the textural and structural integrity of Lysine modified kutki millet starch hydrogels. Various kinetic models were fitted to the time-course measurement of shrinkage behavior of both conventionally (CDHG) and freeze-dried (FDHG) hydrogel. Increasing the swelling temperature (5-50°C) showed values of higher molecular weight of polymer chains between neighboring crosslinks (g/mol) for FDHG (9539.59-56,769.72) than CDHG (1096.28-11,420.48). Similarly, mesh size (ξ) was more for FDHG (38.63-109.53 Ȧ) than CDHG (10.97-42.74 Ȧ). However, other network parameters such as polymer volume fraction ( ) was lower for FDHG (0.229-0.146) than CDHG (0.3882-0.222). These values suggest low swelling power of CDHG compared to FDHG. Thermodynamically, FDHG took less energy to swell than CDHG. The study showed that FDHG has better properties than CDHG and could be employed in nutraceutical delivery. The online version contains supplementary material available at 10.1007/s13197-024-05953-x.