Abstract This article is focused on proposing a novel approach to determining flood mitigation practices based on coupled hydrodynamic and rainfall-tracking models. V-shaped and Baogaisi catchments were applied to assess the effects of the novel approach in mitigating peak discharge and runoff volume, respectively. Specifically, traditional afforestation scenarios were planned from downstream to upstream, while novel afforestation scenarios were designed based on the maximum and minimum contribution rate of sub-areas. Then two types of cases were simulated by the coupled hydrodynamic and rainfall-tracking model again to evaluate the mitigating effects of different afforestation practices. Results show that the coupled model is able to obtain accurate hydrodynamic and rainfall-tracing information simultaneously within each computing grid under the flooding caused by rainfall events. Moreover, in comparison with the reduction effects of traditional cases, results simulated under two catchments illustrated that the novel approach is able to determine spatial prioritization of afforestation management practices. In particular, there is a positive correlation between the contribution rate of afforestation area and the reduction effect of runoff volume caused by rainfall events. Thus, the research could provide a more scientific and reasonable guide in determining spatial prioritization flooding mitigation practices for planners and governments.