In Japan, the road traffic network infrastructure, driven by escalating traffic demand and urbanization, has precipitated a rise in rockfall incidents. Therefore, falling rock protection nets have been deployed, necessitating a rigorous evaluation of their structural load-bearing capacities. This study presents a simulation of a full-scale falling rock protection net using the 3D-distinct element method (3D-DEM). In addition, the proposed method reproduced the unevenness in representing the planar clump model. First, a collision experiment was performed in advance, the dynamic deformation process of the wire net was recorded using video and a high-speed camera, and the tension of the wire ropes was measured. Second, the net and wire ropes were modeled using cylindrical and spherical elements. The reproducibility of the analysis results was examined by comparing with the experimental results. Therefore, the interlocking between the wire and dead weight and the relationship between the impact load and time in the experiment can be represented by the proposed method. The results showed that local deformations around the impact area caused by a heavy-weight collision spread within the protective net, and demonstrated that ropes far from the impact point experienced delayed maximum tension owing to wave propagation.