The resistant starch (RS) in enzymatic branch-chain elongated waxy corn starch (WCS) was separated by using in vitro digestion method. Then, the physicochemical properties and molecular structure of RS were characterized. The results showed that the morphology of starch was significantly changed after digestion, and irregular cracks appeared on the surface of RS. Moreover, the improvement of thermal stabilities of RS wasalso observed. These results revealed that the amorphous regions of modified starches were preferably to be hydrolyzed during digestion. Compared to modified WCS, the molecular weight of RS was profoundly decreased (6.03×10⁶～1.13×10⁸ g/mol). In addition, the peak value of branch chain length distributions of RS varied from DP 26 to DP 31, and the very long chains were almost disappeared. Thus, it was suggested that a particular region of chain is favored in formation of resistant starch.