Check-dams are structures used extensively around the world for soil and water conservation. However, existing models for check-dams are unable to simulate the Sediment Trap Efficiency (STE) at the catchment scale. A numerical model was developed to simulate the SEdiment Deposition upstream of Check-Dams (SEDCD) and integrated into a distributed sediment yield model, the Digital Yellow River Model (DYRIM). Two versions of the SEDCD model were evaluated: the SV version which used the Saint–Venant equation to simulate the unsteady flow, and the BW version, which used a modified backwater equation (based on a quasi-steady approximation) to improve computational efficiency. Sediment deposition and the associated bed profile adjustment were simulated with the sediment conservation equation and the non-equilibrium suspended sediment transport equation. The SEDCD model was first validated in the laboratory using experimental data from a scale-down check-dam. The bed profiles predicted using both versions of the SEDCD model showed good agreement with the observations, with NSE values over 0.9 in most profiles. When integrated into the DYRIM and applied to the Xiaoli River Basin (818 km²) on the Loess Plateau, which has 183 active check-dams, the SEDCD-DYRIM combination predicted the STE for an extreme rainstorm event in 2017 with good accuracy and high computational efficiency. The SEDCD-BW-DYRIM simulated the hourly discharge and sediment concentration with high accuracy (NSE values of 0.79 and 0.71, respectively) and provided single-event STEs (R² value of 0.99) comparable to those of the SEDCD-SV model, with an approximately 30 times faster runtime efficiency than the SEDCD-SV model. The SEDCD-BW model is a powerful and efficient tool to assess the effect of check dams on sediment dynamics at the catchment scale.