In the Yarlung Zangbo River valley in north Himalaya, many high-frequency debris flows develop, with large amounts of run-out debris materials. To reduce the hazard scale of the debris flow, check dams are frequently used to mitigate and prevent debris flow movement, and many check dams are damaged under the impact of debris flows. This paper proposed a novel integrated three-dimensional numerical approach to quantitatively assess the dynamic process of a debris flow and its interaction with a check dam considering check dam damage. The numerical approach is based on the SPH-FDEM method, which uses the SPH of Bingham fluid to simulate debris flows while using the FDEM to simulate structural check dams composed of rock blocks. A test of granular flow impact measurement in an inclined flume was used to validate the rheological characteristics of the debris flow and its interaction with the structure. The debris flow in the G62 gully, which is near NR 318 and has the potential to destroy the road, is used as a case for numerical simulation. Several different engineering conditions, including without a check dam, with an undamaged check dam and with a damaged check dam, were considered. The simulation results show that the debris flow scale without considering the check dam is consistent with the field investigation. The run-out speed, viscous dissipation energy, and frictional energy of the debris flow with time can be quantitatively acquired. When a check dam is considered, the processes of the dam undergoing debris impact, fracture generation and evolution, the separation of broken blocks from the main check dam body, and the transport of these blocks by the debris flow can be clearly observed. The stress, damage area, damage extent, damage mode, fracture energy, and fracture area of the check dam can be quantitatively acquired from the model, which greatly expands the applicability of debris flow numerical models.