Aiming to resolve the practical problem of brown rice kernels being easily broken due to overprocessing during processing (milling and polishing), brown rice kernels of Japonica rice, after hulling, were used as the research object in this study. Firstly, through a texture meter test, the discrete element bonding parameters (Kn is normal stiffness per unit area, Kτ is tangential stiffness per unit area, Cn is critical normal stiffness, Cτ is critical shear stiffness) were obtained. Secondly, a brown rice kernels’ bonding particle model was established by EDEM, and then a second orthogonal rotational combination test was carried out to calibrate the discrete bonding parameters, Kn = 4.43 × 1012 N/m3, Kτ = 6.13 × 1011 N/m3, Cn = 2.55 × 107 Pa, and Cτ = 7.92 × 107 Pa. The error of parameter calibration was within 5%, and the results were able to reflect the actual situation more realistically. Finally, analysis of the crushing process of brown rice kernels showed that their ability to withstand shear damage was not as great as their pressure-bearing capacity. The design of the relevant mechanism and the setting of parameters should be based on the critical shear stiffness of brown rice kernels, and the actual shear force Fτ* set during the processing should be smaller than the theoretical critical shear force Fτ (Fτ* < Fτ = 9.11 N). This study can provide a theoretical basis for optimizing the key structure and operating parameters of rice milling machines and polishing machines to effectively solve the practical problem of increased crushing of brown rice kernels due to overprocessing.