Investigation on amylopectin molecular structure is gaining importance for understanding starch property. Lotus seeds are a novel starch source with high apparent amylose content. Current understanding on the molecular structure of amylopectin in lotus seed starch is scarce. This study compared the molecular structure of a range of lotus seed amylopectins with those of maize and potato amylopectins. Internal structures of these amylopectins were compared via investigating the chain length distribution of their β-limit dextrins. The average lengths and molar compositions of unit chains in lotus seed amylopectins and their β-limit dextrins fell generally between those of maize and potato. The average chain lengths of lotus seed, maize, and potato amylopectins were 19.95 (on average), 19.11, and 21.19 glucosyl residues, respectively. Lotus seed amylopectins had higher weight proportion of clustered unsubstituted chains (44.94 % on average) than those of potato (43.99 %) and maize amylopectins (42.95 %). Results of correlation analysis indicated that apparent amylose content of LS was related to structural characteristics of its amylopectin due to the presence of long external chains. The results of this study are of fundamental importance for the utilization of lotus seed starch as a novel starch source.