Analyzing the characteristics and causes of runoff variation in a typical small basin is beneficial for ecological restoration in the Loess Plateau. This study employed a series of statistical methodologies to examine the characteristics of meteorological changes and underlying surface evolution in the Qishui River Basin (QRB). To differentiate the impacts of climate change and human activities on runoff variation, we applied the Choudhury–Yang formula and the Double Mass Curve (DMC) method. Subsequently, by incorporating future watershed protection strategies and various SSP scenarios, we utilized the Soil and Water Assessment Tool to simulate future runoff while employing the DMC to identify underlying causes of runoff variation. The results suggested that human activity has a slightly greater impact than climate change on reducing runoff during the historical period, with only a 1% difference. However, this will change in the future as human impact becomes increasingly significant. Human activities such as afforestation have dual effects, encompassing positive effects such as improving water quality and mitigating soil erosion, as well as negative consequences such as diminishing local water availability and exacerbating drought. Effective policies should be implemented, involving the use of appropriate tree species and planting methods, finding an appropriate value of forest area, monitoring and evaluation, etc., in order to ensure that the policies are aligned with the broader social, economic, and environmental goals of the QRB. These findings provide valuable guidance for policy-makers in developing management strategies for future environmental changes.