Following large-scale vegetation restoration on the Loess Plateau, vegetation cover has increased markedly, but the mechanisms driving vegetation drought have become more complex under climate change. Precipitation has long been viewed as the dominant control on vegetation drought in arid and semi-arid regions, yet this perspective cannot fully explain the coexistence of sustained vegetation greening and increasing atmospheric aridity. Here, we developed a Standardized Vegetation Water Deficit Index (SVWDI) based on the balance between vegetation water supply and demand, and combined it with grid-based random forest regression and cross-wavelet transform analysis to quantify the effects of meteorological factors and atmospheric circulation on vegetation drought during 1991–2020. Results showed that vegetation drought on the Loess Plateau generally alleviated over the past three decades, but exhibited clear spatiotemporal heterogeneity. More importantly, its dominant drivers shifted fundamentally over time: precipitation dominated during the early stage of the Grain for Green Project, whereas vapor pressure deficit (VPD) and Carbon Dioxide (CO₂) became the leading factors in recent years. In addition, large-scale atmospheric circulation, particularly the Western Pacific Subtropical High, significantly influenced vegetation drought by regulating summer hydrothermal conditions. These findings highlight the increasing importance of plant physiological processes in vegetation drought and suggest that future ecological assessment and management should move beyond a purely hydrological perspective toward a plant physiological–hydrological coupling framework.