Baffle system is a promising disaster mitigation measure, while the mechanism of debris-baffle interaction at grain scale has not been fully understood, and especially the effect of the unsteady nature of granular flow on debris-baffle interaction has not been detailly investigated. For this purpose, we conducted various small-scale model tests and used the three-dimensional discrete element method to assist the interpretation of the experimental results and extend research content. The granular arch that is formed between the baffle slit controls the debris-baffle interaction, which is completely different from the dead zone-dominant debris-barrier interaction mechanism represented by a rigid or flexible barrier. The particle size effect is controlled by the baffle jamming behavior. Larger particles facilitate the rapid formation of a stable force arch with larger energy-breaking efficiency. And flows with larger Froude number are not easy to form stable granular arches. Thus, the baffle array number, particle size, and construction site control the efficiency of baffle structure in deceleration of granular flows. Particularly, increasing the baffle array number restricts the recovery of flow mobility after the flow passes the baffle structure. In general, the construction of baffle at deposition area may not be an effective engineering options, because the impact force discrepancy on baffle array is larger by 28%, the generated energy dissipation is lower by 60.97%, the run-out distance by 10% and the spreading distance on the slope by approximately 40% for baffles in the deposition area compared with baffles constructed on slope.