Rockfall disasters are frequently observed and are considered serious hazards in the mountainous regions of western China. Due to the variable geometric shapes and complex incident spatial states of falling rocks, their trajectories are difficult to predict, which poses significant challenges for the dimensional design and spatial arrangement of conventional linear protective structures. The discrete element method (DEM) was employed to develop a two-stage numerical model for simulating the interaction between rockfalls and protective structures. The model was calibrated using parameters derived from laboratory and field experiments, as well as site investigation data. The influence of rock geometry (ellipsoidal shapes) and incident spatial conditions (initial angles and velocities) on rockfall trajectories, rebound heights, and lateral deviations was systematically investigated. The results indicate that variations in rock shape primarily affect trajectory behavior through centroid offset and differences in rotational inertia, whereas the initial angle and velocity mainly govern the divergence of movement direction and the rate of energy dissipation, respectively. Based on the analysis of trajectory distribution bandwidths, it is proposed that protective structures should be installed beyond the toe of the slope and extended into a defined buffer zone. A case study verified that this optimized layout strategy can reduce the effective coverage area of protective structures by 41%, providing a computationally efficient and accurate approach for rockfall mitigation in complex terrain.