Study region: This study focused on the Yangguan plot (94.21 degrees E, 40.00 degrees N; 650 & times;750 m) in the hyper-arid Gobi Desert of Inner Asia. Study focus: Vegetation distribution results from combined ecological factors. Traditional research emphasized macro-scales (e.g., satellite remote sensing), with less attention to micro-scale heterogeneity, particularly in hyper-arid regions. In this study, we employed Unmanned Aerial Vehicle (UAV) photogrammetry to achieve decimeter-resolution microtopography reconstruction in the study plot. Using a suite of microtopographic and hydrological indicators together with statistical models, we examined the relationships among microtopography, hydrology, and vegetation. New hydrological insights for the region: We proposed a new high-precision analytical approach for microtopography-hydrology-vegetation effect based on UAV photogrammetry, which can serve as a methodological reference for future research. We also proposed a cross-scale conceptual model: Vegetation pattern = Macro-environmental baseline + Micro-environmental redistribution. The key process of micro-environmental redistribution in hyper-arid regions is the microtopography-hydrology (water redistribution)-vegetation (distribution pattern) effect, which includes that windward/leeward slopes affect water vapor input, sunny/shady slopes influence moisture evaporation, and topographic relief and slope affect surface runoff. Additionally, vegetation coverage increases in windward/shady slopes and catchment areas, but avoids the valley bottoms due to excessive hydrological disturbance, exhibiting a "rise-then-fall" trend. This study reveals how hydrological processes mediated by microtopography regulate vegetation distribution patterns in hyper-arid environments.