In recent decades, both observation and simulation data have demonstrated an obvious decrease in runoff and soil moisture, with increasing evapotranspiration, over the Loess Plateau. In this study, we employed a Variable Infiltration Capacity model coupled with scenario simulation to explore the impact of change in climate and land cover on four hydrological variables (HVs) over the Loess Plateau, i.e., evapotranspiration (ET), runoff (Runoff), shallow soil moisture (SM1), and deep soil moisture (SM2). Results showed precipitation, rather than temperature, had the closest relationship with the four HVs, with r ranging from 0.76 to 0.97 (p < 0.01), and this was therefore presumed to be the dominant climate-based driving factor in the variation of hydrological regimes. Vegetation conversion, from cropland and grassland to woodland, significantly reduced runoff and increased soil moisture consumption, to sustain an increased ET, and, assuming that the reduction of SM2 is entirely evaporated, we can attribute 71.28% ± 18.64%, 65.89% ± 24.14% of the ET increase to the water loss of SM2 in the two conversion modes, respectively. The variation in HVs, induced by land cover change, were higher than the expected climate change with respect to SM1, while different factors were selected to determine HVs variation in six catchments, due to differences in the mode and intensity of vegetation conversion, and the degree of climate change. Our findings are critical for understanding and quantifying the impact of climate change and vegetation conversions, and provide a further basis for the design of water resources and land-use management strategies with respect to climate change, especially in the water-limited Loess Plateau.