The crystalline and structural properties of acid-modified C-type starch from lotus rhizomes were investigated using a combination of techniques. The degradation of granule during hydrolysis began from the end distant from the hilum and then propagated into the center of granule, accompanied by loss of birefringence. The crystallinity changed from C-type to A-type via CA-type during hydrolysis. At the early stage of hydrolysis, the amylose content substantially reduced, the peak and conclusion gelatinization temperatures increased, and the enthalpy decreased. During hydrolysis, the double helix content gradually increased and the amorphous component decreased, the lamellar peak intensity firstly increased and then decreased accompanied by hydrolysis of amorphous and crystalline regions. This study elucidated that B-type allomorph was mainly arranged in the distal region of eccentric hilum, A-type allomorph was mainly located in the periphery of hilum end, and the center of granule was a mixed distribution of A- and B-type allomorphs.