Identifying the spatial and temporal heterogeneity of water-related ecosystem services and the mechanisms influencing them is essential for optimizing ecosystem governance and maintaining watershed sustainable development. However, the complex and undiscovered interplay between human activities and natural factors underpins the solutions to the water scarcity and flooding challenges faced by climate transition zone basins. This study used a multiple spatial-scale analysis to: (i) quantify the spatial and temporal variations of the water yield ecosystem service (WYs) of the Wei River Basin (WRB) from 2000 to 2020 using the InVEST model and remote sensing data; and (ii) look at how human activities, climate, topography, and vegetation affect the WYs at the climate transition zone sub-catchment scale using the geographical detector model and multi-scale geographically weighted regression (MGWR). The conclusive research reveals that there would be a gradual increase in WYs between the years 2000 and 2020, as well as a distinct and very different spatial aggregation along the climatic divide. The average yearly precipitation was shown to be particularly linked to the water yield of the WRB. The interplay of human, climatic, plant, and terrain variables has a substantially higher influence than most single factors on the geographical differentiation of WYs. Bivariate enhancement and non-linear enhancement are the most common types of factor interactions. This shows that there are significant interactions between natural and human variables. Our study shows that precipitation and temperature are the main factors that cause WYs in the semi-arid zone. In the semi-humid zone, precipitation and vegetation are the key controlling factors that cause WYs. We provide new perspectives for understanding and optimizing ecosystem management by comparing the drivers of WYS in sub-basins with different climatic conditions. Based on the findings, we recommend that particular attention should be paid to ecosystem restoration practices in watersheds in climatic transition zones.