Herein, oxidation and carboxymethylation were employed to improve the dispersibility and stability of starch nanocrystal (SNC) in aqueous solution by enhancing intermolecular electrostatic repulsion between SNCs, as well as to promote their protein loading capacity. FT-IR, XPS, and NMR analyses confirmed the successful surface modification of SNC, with oxidation likely occurring at the C6-OH position of anhydroglucose units. Oxidation selectively degraded the amorphous parts with small molecular weight, while carboxymethylation removed surface hydrocarbons, promoting relative crystallinity, crystalline lamellae thickness, and structural compactness in the oxidized and carboxymethylated SNC (OSNC and CSNC). Morphologically, OSNC and CSNC exhibited regular square shapes, with CSNC showing a more uniform appearance. Both OSNC and CSNC displayed small hydrodynamic size and high zeta potential, along with high transparency suspensions at pH 7, indicating good dispersibility and stability driven by electrostatic repulsion. Only OSNC, with the highest degree of oxidation, maintained stability at pH 3, due to its strong buffer capacity against protonation. Furthermore, both OSNC and CSNC showed enhanced protein loading capacity, with OSNC achieving higher capacity than CSNC, suggesting its potential as a protein delivery carrier. This work offers alternative strategies to reduce interparticle aggregation in SNCs, broadening their industrial applications.