To build a DEM model of Cyperus esculentus seed particles, the shape and size of the Cyperus esculentus seed particles were measured and analyzed. The results showed that the dispersity in size had a normal distribution. Additionally, a certain functional relationship between the primary dimension and secondary dimensions was determined. The width of the seed was the primary dimension, and the other secondary dimensions (length and thickness) were calculated based on their relationships with the primary dimension. On this basis, an approach for modeling Cyperus esculentus seed particles based on the multi-sphere (MS) method was proposed. The discrete element analysis models of three varieties of Cyperus esculentus seeds were established with different numbers of filing spheres. Moreover, to obtain more accurate simulation parameters, first, a range of values of the simulation parameters was obtained by the experimental method. Second, the Plackett−Burman (PB) test and the path of steepest ascent method were both adopted to correct and calibrate the simulation parameters, which were difficult to obtain through experiments, and simulation of the direct shear test was used for calibration. All of the methods guaranteed that the selected parameters were reasonable. The test results showed that the static friction coefficient of seed−seed had a significant effect on the simulation results. Finally, piling tests and the bulk density test were used for modeling verification. By comparing the simulated results and experimental results in the piling tests and bulk density test, when the number of filing spheres increased, the simulated results were close to those obtained experimentally. Therefore, the feasibility and validity of the modeling method for Cyperus esculentus seed particles that we proposed and the simulation parameters that were obtained were verified.