In this study, P. rotundifolius starch, a new source of starch, was subjected to HMT, citric acid, and HMT-citric acid modification and studied the change in crystalline pasting and functional properties and in vito digestibility. XRD showed an A-type diffraction pattern to the native starch and was unaffected by all modifications. The relative crystallinity and the gelatinization enthalpy significantly decreased (p ≤ 0.05) on dual modification. A new peak at 1724 cm⁻¹ was observed in the FT-IR spectra of citric acid modified starch, and the intensity of the peak became stronger in HMT followed by citric acid starch, which was consistent with the results of degree of substitution. Native starch showed a peak viscosity of 3343 cP and significantly decreased on citric acid modification, and HMT treatment increases the effectiveness of the citric acid modification. The in vito digestibility of P. rotundifolius starch was significantly affected by both single and dual modifications. The crystalline destruction in starch granules during HMT enhanced the substitution of citrate in the starch granule, improving the SDS and RS percentage in dual modified starch. The HMT-citric acid dual modification method was shown to modify starches with different properties and could be used as a substitute for producing low glycaemic index foods.