Current understanding of physicochemical properties of lotus seed starch (LS) is scarce partly due to its largely unknown molecular structure. This study compared the physicochemical and molecular characteristics of LSs of a wide collection to those of conventional starches (potato (PS) and maize starches (MS)). Variations were found in the chemical composition, physicochemical properties, and molecular structure of LSs. Amylose content and weight-based ratio of short to long chains of amylopectin (APS:APL) were principal factors affecting the physicochemical properties of LSs from different origins. Compared with PS and MS, LSs had higher gelatinization temperatures, lower amylose leaching, and faster retrogradation. These unique properties of LSs were related to their molecular structure and chemical composition. LSs had higher amylose contents than PS and MS as evaluated by various methods. A majority of amylose chains in LS were longer than those in MS but were shorter than those in PS. The APS:APL of LSs were higher than that of MS but lower than that of PS. The results provided a structural basis for understanding the properties of LS and suggested that this unconventional starch may be complementary to conventional starches for industrial applications.