As well as the damage to membrane structures caused by direct wind forces-either overstressing under peak loads, or fatigue damage under fluctuating loads of a lower level, a major cause of damage is flying debris in strong wind conditions. Penetration of the membrane by wind-borne debris will change the load transfer route of the structure and greatly amplify the internal pressure, which may result in progressive collapse of the whole structure. This paper addressed the flight generation, flight path and impact of wind-borne debris to pre-stressed membrane structures with the purpose to investigate the risk of wind-borne debris to this kind of structures in certain regions. The flight speed threshold was discussed, following the simulation of debris trajectory in terms of equations of motion. The simulation results were compared with existing experimental data, which showed good agreement to each other. Finally, the penetration of membrane by debris was simulated through a finite element analysis. This study presented an integrated simulation framework to assess the impact of wind-borne debris on membrane structures.