Multi-layer rigid netting barriers (RNBs) can obstruct the granular flow layer by layer, and all the layers of the structures share the impact load, which has better reliability than single-layer structure. However, the granular flow obstructed by multi-layer RNBs is complicated. The grains between the layers of RNBs may make the forces acting on all structures related to each other. Under the limited testing conditions, it is difficult to obtain several important information such as the obstruction efficiency of structural barriers and the impact forces acting on the RNBs at all layers. In this study, the discrete element method is used to numerically simulate a typical granular flow experiment. Based on the numerical verification, the method was used to study the mechanical characteristics of the RNBs at all layers and the typical process of granular flow under different settings. The results show that the numerical calculation can not only simulate the rebound, run-up, splash, passing-through and other movements of grains during the obstruction process, but also obtain the mechanical characteristics of the RNBs at all layers that are related to each other caused by the grains between the RNBs, and the final deposition of grains in front of the RNBs. The mesh and position settings of the protective structures have a significant influence on the forces acting on the RNBs at all layers, so adjusting the RNB settings through numerical optimization can make the forces on RNBs more reasonable and optimize the design of the protective structures. At the same time, the grain segregation characteristics in front of the RNBs obtained by the numerical simulation can provide a basis for further research on the physical and mechanical characteristics and the stability of the deposition.