The rich active hydroxyl groups on starch nanocrystals (SNC) surface limits its dispersion and stability in the aqueous phase. To address this issue, ozone modification for 0 (SNC), 0.5 (SNC-1), 1 (SNC-2), 1.5 (SNC-3), and 2 h (SNC-4) as compared to conventionally chemical methods was applied to functionally modify the SNC. The impact of ozone treatment on the structural and surface characteristics of waxy rice starch nanocrystals. The findings revealed that longer ozone treatment durations favored the formation of carbonyl groups in starch molecules. Initially, ozone oxidized the hydroxyl group of the macromolecule. Once the carbonyl groups formed, the cross-linking reaction occurred among starch nanocrystals through condensation reactions, leading to the increasing molecular orderliness. X-ray photoelectron spectroscopy, X-ray diffraction and Small-angle X-ray scattering analyses of SNC-2 supported this finding with a reduced O/C ratio, and implied that surface oxidation did not alter the crystal type but rather enhanced molecular hydration in an aqueous system, leading to increased interfacial thickness and fractal dimension. Additionally, ozone oxidation improved surface properties such as charge and hydrophobicity. Oxidized SNC also exhibited altered gelatinization properties due to surface degradation. This study offers a promising strategy for enhancing SNC surface properties, crucial for food science applications.