UP-LRS3 exhibited the strongest iodine absorption ability and thermostability, which were affected by the degree of polymerization and degree of double helical structure,respectively. The different physicochemical properties of GP-LRS3, MP-LRS3 and UP-LRS3 were attributed to their different structure. Interestingly, the property was a result of a combination of multiple factors. The result will provide the background and practical knowledge for the application of lotus seed resistant starch. MP-LRS3 could be explored as a prebiotic and UP-LRS3 was a potential thermal stabilizer in food industries.