•We demonstrate how the mechanistic modeling method has the potential for characterizing ecosystem service flows.•The flood mitigation ecosystem service was quantified by coupling hydrological and hydrodynamic models.•The quantification takes into account the linkages between the flood’s supply part and the benefit part.•Calibrated mechanistic models hold the promise of providing an accurate basis for quantifying service flows. Flood mitigation service provides crucial information for reducing flood disasters and assessing ecosystem capacities by quantifying how much damage is reduced and how many benefiting areas are protected during flood events. However, there remains a gap in the full-process quantification, which results in less precise simulation outcomes. In this study, we introduce a novel methodology to accurately quantify the flood mitigation service of ecosystems by coupling hydrological and hydrodynamic models. We utilized the Hydrological Simulation Program-Fortran (HSPF) model to simulate peak flow and flood volume and then used these data as inputs for the Environmental Fluid Dynamics Code (EFDC) hydrodynamic model to simulate the spatial extent and depth of flood inundation. The contribution and capacity of the ecosystem are reflected through the reduction in peak flow, flood volume, and inundation areas. We used the Nandu Basin flood event in October 2010 as a case study to illustrate our approach, comparing our assessment results with those simulated by the Integrated Valuation of Ecosystem Services and Tradeoffs (InVEST) model and the Height Above Nearest Drainage (HAND) model. The results demonstrate that coupling the HSPF model (R2 = 0.93) with the EFDC model (overlap ratio = 83.71 %) allows for precise quantification of flood mitigation service. The process-based hydrological and hydrodynamic models show a high correlation with the simpler and faster InVEST and HAND model simulations, with the full-process models reducing relative errors by 7.66 % and 5.25 % respectively. This study offers a promising approach for accurately and comprehensively assessing flood mitigation ecosystem service and provides a basis for model selection.