Flexible barrier structures are commonly installed in mountainous regions to resist the impact effects of rock avalanches. Without reliable physical data, the study of rock landslide initiation and the impact mechanism of avalanche debris flow under seismic excitation remains poorly understood. In this study, a model of rock slope-flexible barrier system was developed to simulate seismic slope failure behavior and debris flow impact on flexible barriers. Seismic waves in shaking table tests were triaxially loaded to effectively simulate actual seismic responses. The results indicate that the response of the Acceleration Amplification Factor (AAF) is closely associated with seismic damage and deformation within the overlying rock layers and differential propagation of seismic energy on either side of the shear band triggers rockslide initiation. Furthermore, the progressive failure mode of modeled slopes under multiple seismic events is slip-compression cracking failure. Crushing spreading at the intersection of the cracking and slip surfaces is the source of the loose fractured rock mass. Finally, this paper examines the impact patterns and dynamic responses of large individual blocks and loose fractured deposits on flexible barriers. Large blocks cause localized strong acceleration in the steel wire nets, increasing the risk of local damage, whereas loose deposits tend to induce overall seismic deformation and instability of the supporting structure. The natural seismic damage mechanisms of the barrier structure are revealed. It is recommended that flexible barrier structures in earthquake-prone mountainous areas incorporate a reasonable footing design to ensure the columns can deflect out-of-plane in response to seismic activity.