Complex starch is gaining research attention due to its unique physicochemical and functional properties. Lotus seed starch (LS) suspensions (6.7%, w/v) with added green tea polyphenols (GTPs) (10%, w/w) were subjected to ultrasound (200-1000 W)-microwave (150-225 W) (UM) treatment for 15 min. The effects of UM treatment on the physicochemical properties of the LS-GTP system were investigated and exceeded that of microwave or ultrasound alone. The properties (morphology, X-ray diffraction pattern and so on) were affected by GTPs to various extents, depending on ultrasonic power. These influences may be explained by the non-covalent interactions between GTPs and LS. V-type LS-GTP inclusion complex and non-inclusive complex formation were observed. Their morphology and the distribution of GTPs molecules within them were estimated using scanning electron microscopy and confocal laser scanning microscopy. Furthermore, the digestion of LS-GTP complex was investigated by a dynamic in vitro rat stomach-duodenum (DIVRSD) model, lower digestion efficiency of LS has been achieved and the residues showed gradual improvement in morphology. These all experimental results do provide new insight into the complex starch production.