Dioscorea alata Linn. (D. AL) rich in starch was widely used as food and medicine. This work aimed to compare the effect of acid and glucoamylase on the starch of different reaction time. The physicochemical properties of the native and hydrolyzed starches, such as swelling power (SP), starch solubility (SOL), and paste clarity were also determined in this study. The native and modified starches by acid and glucoamylase were compared and characterized by scanning electron microscope (SEM) and secondary derivative FT-IR spectroscopy. The morphological characteristics of native D. AL starch granules revealed by SEM varied from round to oval or elliptic with smooth surface. SEM showed that glucoamylase primarily attacked the exterior of starch granules and permeate into the interior by the cracks formed on the surface. Owing to acid hydrolysis, the starch granules were depressed and transformed to bread-like in shape and then broke into irregular lumps with particles adhered. From secondary derivative FT-IR spectrum, the intensities of the two peaks from acid and enzyme hydrolysis starches at 1137 and 1066/cm were stronger than native starch. Some new peaks appeared due to hydrolysis. The digested starches exhibited a lower SOL and SP than native starch in water as the temperature increasing. The light transmittance of the digested starches was significantly higher than that of native starch paste and decreased with increase in storage period.