On catchment scales, sediment discharge depends on both sediment transport capacity and sediment availability. The quantification of sediment discharge at the regional scales is important but is rarely adequately represented in regional hydrological models. Here, we introduce a regional water erosion and sediment transport model, Atmospheric and Hydrological-Sediment Modeling System (AHMS-SED). This model integrates the Atmospheric and Hydrological Modeling System (AHMS) with the improved CASCade 2-Dimensional SEDiment (CASC2D-SED) model and incorporates gully erosion as a significant factor affecting sediment supply. A gully area index is introduced to quantify the fraction of the gully area and the enhancement of water erosion induced by concentrated flow in gullies. We use the AHMS-SED to simulate the sediment processes in the Yellow River Basin from 1979 to 1987 at a 20 km resolution. We find quantitative agreement between the observations and model predictions for monthly sediment fluxes at five major hydrological stations along the Yellow River, with excellent performance metrics (modified Kling-Gupta efficiency = 0.90, Nash-Sutcliffe model efficiency coefficient = 0.81) at the basin outlet. The results demonstrate the strong performance of the AHMS-SED and the robustness of the sediment supply estimates. We also use AHMS-SED to investigate how changes in climate and human activities affect sediment discharge in the Yellow River. The model shows that halving precipitation intensity substantially reduces sediment discharge, halving precipitation amount reduces it by 60%, and doubling irrigation reduces it by 10%.