Discrete element method (DEM) is a powerful modeling tool widely used to simulate agricultural production processes. DEM simulations provide both qualitative and quantitate information on particle flow, which helps designers gain a better understanding of the system mechanism and aids the optimization of the design. The accuracy of the DEM simulations model is greatly affected by the model parameter values. However, precisely quantifying the physical properties of the grain kernels into the model parameter values remains a challenging task due to the irregular shape of the kernel and the heterogeneity of the biological material. In this study, new methods of determining the physical properties of corn and wheat kernels for DEM simulations were proposed to give an accurate estimation of the model parameter values. X-ray micro-CT scanning method was used to acquire the particle shape representation of the grain kernels. The coefficient of restitution was measured by a calibration method with a box containing multiple bins. The coefficient of friction was determined by reciprocating friction test. The measured model parameter values were used to simulate common bulk material tests, i.e. bulk density test, angle of repose test, and tilting box test. The comparison was made between the simulated results and the experimental measurements.