The water yield (WY) service is a critical ecosystem service in arid regions, and understanding its spatiotemporal heterogeneity and controls is important for sustainable watershed management. Annual water yield (WY) in the Aksu River Basin (ARB), China, from 2000 to 2020 was simulated using the InVEST model, with validation against observed runoff (NSE = 0.840, R2 = 0.846, RMSE = 1.787). The results revealed a decline in WY from 66.49 mm in 2000 to 43.15 mm in 2015, while retaining a clear north-south gradient, with higher values in the north. Areas showing decreasing and increasing trends accounted for 45.34% and 3.14% of the basin, respectively. WY exhibited strong spatial autocorrelation (global Moran's I = 0.912-0.941), with high-value clusters in the north and low-value clusters in the south. GeoDetector identified precipitation, temperature, and potential evapotranspiration as key drivers (q = 0.889, 0.880, and 0.832, respectively), with precipitation-related interactions generally exceeding 0.9, indicating enhanced explanatory power through multi-factor coupling. After variable screening and collinearity control, MGWR revealed spatially varying effects of drivers and significant spatial non-stationarity. Overall, despite the declining trend, WY in the ARB maintained a relatively stable spatial structure, with its heterogeneity primarily driven by the coupling of climatic forcing and topographic constraints, providing a scientific basis for zonal water resource management in arid river basins.