The effects of oxidation by sodium hypochlorite (0, 0.8, 2, and 5%, NaOCl), the presence of endogenous proteins, and amylose content on waxy and common rice flours (WF, CF) and starches (WS, CS) were investigated in terms of in vitro starch digestibility, morphology and surface properties, and thermal and rheological characteristics. The concentration of NaOCl had an effect on all the samples including WF, CF, WS, and CS. The carbonyl and carboxyl group contents increased up to 25 and 10 folds (P < 0.05) of oxidized starches (WS, CS), respectively. Only mild oxidation (P < 0.05) occurred in flours (WF, WS). In addition, endogenous proteins were oxidized according to amino acid analysis and SDS–PAGE results. Glu+Gln, Gly, His, Arg, Tyr, and Lys were more sensitive to NaOCl oxidation. Disulfide bonds, hydrophobic force, and hydrogen bonds were involved in protein polymerization after NaOCl oxidative modification. In granular state, the in vitro starch digestibility of WF, WS, and CS decreased by 5% NaOCl oxidation. After gelatinization, only 2 and 5% oxidized WS had lower digestibility. Scanning electron microscopy and confocal laser scanning microscopy further demonstrated that protein existed on the surface of starch granules and had aggregation by oxidation. X-ray diffraction patterns showed the crystallinity of 5% oxidized flours and starches was reduced compared with all their non-oxidized samples. Thermal and rheological properties were analyzed by differential scanning calorimetry and rheometer, respectively. Starch gelatinization peak temperature of flours (WF, RF) was increased by 3 °C, but starches (WS, CS) had a significantly decrease by 8 °C. Viscoelastic patterns were dramatically changed by oxidation. Oxidized WF and CF had increased in both viscosity and elasticity by oxidation, whereas both WS and CS had significantly lower viscoelasticity after oxidative modification.