In semi-arid agro-pastoral ecotones, the conflict between agricultural water demand and ecological water security is intensifying under changing climate conditions. Understanding the driving mechanisms of runoff depletion is critical for sustainable agricultural water management. Focusing on the Xiliao River Basin, a typical semi-arid region in China, this study quantified the contributions of climate change and human activities to runoff reduction from 1980 to 2022 using a Budyko-elasticity framework. The results revealed an abrupt decline in runoff occurring in 2002, with significant spatial heterogeneity characterized as "upstream climate-driven, middle-downstream human-driven". In the upstream areas, precipitation reduction was the dominant driver (contribution: 52.6%-64.1%). Crucially, in the middle and lower reaches, where agriculture is concentrated, changes in underlying surface parameters were the primary factors (contribution: 75.7%-78.9%). By decomposing these parameters, this study confirmed that high-intensity direct water withdrawal for agricultural irrigation, rather than the indirect ecological effects of vegetation restoration, was the fundamental cause of runoff depletion in these sections. Furthermore, a superimposed effect was identified, where upstream climate-induced drought exacerbates downstream water shortages. These findings highlight that controlling agricultural irrigation quotas and implementing precise zoned management are imperative for reconciling agricultural development with river ecosystem health in semi-arid basins.