The structure of rice bran protein obtained from defatted rice bran at various dephenolization times (0, 1, 2, 4, and 6) was examined to determine the impact of the degree of rice bran dephenolization upon rice bran protein structure. The total phenolics content in defatted rice bran and rice bran protein gradually decreased as dephenolization times increased, ranging from 390.12 to 131.16 mg GAE/100 g DW and from 30.80 to 17.85 mg/g, respectively, and the free sulfhydryl content of rice bran protein increased from 16.45 to 28.24 nmol/mg, accompanied by a decrease in surface hydrophobicity and the content of high molecular weight subunits. Furthermore, the maximum intrinsic fluorescence intensity and the flexibility of the secondary and spatial structure of rice bran protein initially increased and subsequently declined, reaching the highest level after two dephenolization cycles, while the absolute value of Zeta potential and particle size initially reduced and subsequently increased, reaching the lowest value after two dephenolization cycles. This study showed that the degree of removal of endogenous phenolics from defatted rice bran had an important effect on the structure of rice bran protein, which provided a more theoretical reference for regulating the structural characteristics of rice bran protein.