Aiming at the lack of intrinsic parameters problem of Panax notoginseng stem, contact parameters between Panax notoginseng stem and operating equipment, when using the discrete element method for simulation analysis of key working processes, such as Panax notoginseng combined harvesting and stem killing. Panax notoginseng stem was taken as the object, the discrete element Hertz-Mindlin/Hertz-Mindlin with bonding of Panax notoginseng stem was established by software EDEM. The parameters of discrete element were calibrated by stacking angle experiment and virtual simulation test, and the seedling killing device model of Panax notoginseng stem was established. The intrinsic parameters of stem of were determined by mechanical properties tests. The pile angle of Panax notoginseng stem was tested by cylinder lifting method, the cylinder lifting method was used to test the stacking angle of Panax notoginseng stem, the stacking angle of Panax notoginseng stem in the physical experiment was 44.53° by performing contour fitting on the stacking angle image with Origin software. The Placktt-Burman experiment, steepest climb test and the Central-Composite experiment were used to determine the contact parameters of Panax notoginseng stem and the operating equipment, and the reliability of the model was verified by the stacking angle test, and the shear test. The results showed that the optimal values of collision recovery coefficient, static friction coefficient and rolling friction coefficient between Panax notoginseng stem and operation equipment were 0.319, 0.25 and 0.029, respectively. The optimal values of collision recovery coefficient, static friction coefficient, and rolling friction coefficient were 0.4, 0.29 and 0.032, respectively. The normal stiffness Kn of the Hertz-Mindlin with bonding model was 3.26×108N/m3, the tangential stiffness Ks was 2.17×108N/m3, the normal critical stress σ was 2.27MPa, the tangential critical stress γ was 9.65MPa, and the bonding radius Rd was 0.1mm. The relative error in the accumulation angle verification test was 0.29%;the relative error in the shear verification test was 1.52%, and the error was small. The discrete element model of Panax notoginseng stem was basically consistent with the actual situation, and the model of Panax notoginseng stem and the calibration of discrete element simulation parameters were reliable, which can provide a reference for the research of discrete element simulation of Panax notoginseng stem.