In order to reduce the digging resistance during Panax notoginseng harvesting, the roots and planting soil of Panax notoginseng were taken as the research object, the intrinsic physical parameters were measured, Bonding parameters were set to establish the discrete element model of roots and stems of Panax notoginseng , and the root and soil bonding mechanism was analyzed. The Hertz-Mindlin with JKR was used to establish the discrete element composite model of roots and stems and planting soil of Panax notoginseng. The theoretical mechanical model of the digging shovel was established and analyzed, and the design model size of the bionic digging shovel was determined as follows: 360mm×150mm×8mm, entry angle of 30°, half angle of the shovel tip of 60°. The point cloud data of the three-dimensional boar head model were collected, the structural curve equation of the bionic shovel was determined, and the three-dimensional model of the bionic excavator shovel was established. The simulation comparison test of bionic excavator shovel and plane excavator shovel was carried out, the average displacement and average excavation resistance were obtained by tracking the particle displacement flow direction, and the drag reduction mechanism of excavation shovel surface was defined by analyzing the particle velocity vector. The drag reduction rate of the bionic excavator was 19.15% in the simulation test. The soil groove test was carried out with high-speed photography equipment and resistance acquisition equipment. The results showed that the flow direction of soil particles was consistent with the simulation trend. The average digging resistance of the bionic excavator and the surface excavator was 1207.23N and 1594.49N, and the drag reduction rate of the bionic excavator was 24.29%, which was very close to the drag reduction rate of the simulation test. It was verified that the discrete element model was accurate and reliable, the mechanical model of excavation shovel was constructed accurately, and the bionic structure design was reasonable.