Abstract: The traditional hydrological design in data-starved areas mostly uses hydrological transfer methods, but due to the spatial heterogeneity of the Loess Plateau, the estimation results often have large errors, and the runoff mechanism in the Loess Plateau area is relatively complex, with strong groundwater recharge, so it is difficult for simple hydrological models to accurately simulate the regional hydrological processes. Given this, this paper takes the Malian River Basin as the study area, implements the hydrological simulation on the scale of the Malian River Basin through the SWAT-MODFLOW coupled model, evaluates the spatial and temporal distribution patterns of its surface water resources under different surface cover and its evolution characteristics, to provide a reference for the evaluation of water resources in the data scarce area represented by the Malian River Basin. The model calibration results show that the constructed SWAT-MODFLOW coupled model has good applicability in the loess plateau represented by the Malian River basin, and the NSE coefficient of the outlet site is as high as 0.92. Compared with the area ratio calculation method commonly used in hydrological design, the spatial distribution results of surface water resources obtained based on the coupled model have more reference value. The spatial heterogeneity of runoff and water production capacity of different sub-basins or regions in the Malian River Basin under near-natural conditions is remarkable. The overall trend of runoff at the outlet section is gradually increasing from northwest to southeast, with the strongest water production capacity in the Dongchuan and Xichuan mainstream areas in the upper part of the basin, the weaker capacity in the upper part of the Huanjiang River, and the water production capacity in other areas between the two. The change of vegetation cover in the basin with the transfer from cropland to grassland and woodland has a limited impact on the surface water resources in the Malian River basin, while the direct human activities in the watershed represented by water extraction have a profound impact on the reduction of runoff.