Many rivers originating from mountainous areas cannot be adequately measured in the field to obtain sufficient basic data due to the challenging terrain, which poses difficulties for conducting relevant research such as hydrodynamic and sediment transport simulations, fluvial material fluxes. This study utilized a combination of 71 river cross sections extracted from multisource remote sensing data and 34 cross sections measured by hydrological stations between 2010 and 2018 to generate generalized cross sections for all river orders in the middle reaches of the Yellow River. By integrating the generalized cross sections, river surfaces, and traditional DEM river network, a comprehensive 3-D river network has been established to provide a more accurate representation of the morphological changes along the river channel. To tackle the challenge of simulating runoff in data-deficient areas, the Digital Yellow River Integrated Model (DYRIM), a potent distributed hydrological model, was enhanced by incorporating geometric parameters derived from a 3-D river network into almost all input parameters that can be obtained from multi-source remote sensing. This enhancement enabled the model to accurately simulate runoff in representative data-deficient rivers of the Loess Plateau. The Nash Efficiency coefficients for the simulated runoff exhibited improvement of 23% compared to previous studies, surpassing 0.8 for the period between 2010 and 2018. Additionally, the simulated errors for flow velocity and water depth were 7% and 9% respectively. This approach can provide essential data for the simulation of hydrological processes and improving hydrological models, as well as technical methodologies for related research such as sediment transport simulations and river carbon emissions.