In this study, mathematical model equations are proposed for synthesis of starch nanocrystals from pearl millet varieties, HHB 67 and ProAgro 9444, differing in amylose content. Acid hydrolysis parameters, temperature, acid concentration, and hydrolysis time are optimized, thereafter, characterization of starch nanocrystals is done. Starch extraction is done by wet milling, yield, and amylose content of 41.23% and 15.05% for HHB 67 and, 45.66% and 20.21% for ProAgro 9444, respectively, are obtained. Rate constant values of kinetic studies reflect dependency of yield on temperature, duration, and acid concentration. Full factorial design is used for obtaining the model equations and optimizing the process parameters. Optimized yield of 19.12% and hydrodynamic diameter of 152 nm are obtained for HHB67 at 3.19 M acid concentration for 3 days at 45 °C, and for ProAgro9444 (15.68%, 200 nm) at 3.24 M acid concentration for 3 days at 45 °C. Yield is less, hydrodynamic particle size is more for ProAgro 9444 as compared to HHB 67. Morphological characteristics reveal irregular polygonal native starch granules whereas nanocrystals are spherical (30–70 nm). The crystallinity index increases appreciably after hydrolysis. No gelatinization behavior is observed in pasting curve for nanocrystals. Moreover, steady shear curves depict pseudoplastic behavior.