Native lotus (Nelumbo nucifera G.) seed starch (LSS) was single- and dual-modified by heat-moisture treatment (HMT), ultrasonication (US), HMT followed by the US (HMT-US), and the US followed by HMT (US-HMT). The modified lotus seed starch (LSS) was evaluated for its physicochemical, pasting, thermal, and rheological properties and in vitro digestibility. All treatments decreased the swelling power (10.52–14.0 g/g), solubility (12.20–15.95 %), and amylose content (23.71–25.67 %) except for ultrasonication (17.67 g/g, 17.90 %, 29.09 %, respectively) when compared with native LSS (15.05 g/g, 16.12 %, 27.12 %, respectively). According to the rheological study, G′ (1665–4004 Pa) was greater than G″ (119–308 Pa) for all LSS gel samples demonstrating their elastic character. Moreover, gelatinization enthalpy (17.56–16.05 J/g) increased in all treatments compared to native LSS (15.38 J/g). Ultrasonication treatment improved the thermal stability of LSS. The digestibility results showed that dual modification using HMT and US significantly enhanced resistant starch (RS) and reduced slowly digestible starch (SDS) in LSS. Cracks were observed on the surface of the modified LSS granules. Peak viscosity decreased in all modified starches except for ultrasonication, suggesting their resistance to shear-thinning during cooking, making them ideal weaning food components. The results obtained after different modifications in this study could be a useful ready reference to select appropriate modification treatments to produce modified LSS with desired properties depending on their end-use.