Highlights What are the main findings? Vegetation drought responses are decomposed into physiological and structural anomalies, revealing fine-scale functional impacts of drought beyond traditional methods. Vegetation physiological components explained most of the functional responses during drought, and physiological anomalies accounted for over 88% of total vegetation anomalies during drought peaks, highlighting their dominant role in early-stage drought response. What are the implications of the main findings? Physiological responses consistently outperform structural responses before, during, and after drought peaks, with intensified fluctuations at peak stress, underscoring vegetation's prioritization of rapid physiological adjustments. This study advocates for the integration of physiological remote sensing indicators to establish a more sensitive early warning system for drought. Spatial vulnerability patterns and quantified climate drivers directly support tailored water and climate adaptation strategies.Highlights What are the main findings? Vegetation drought responses are decomposed into physiological and structural anomalies, revealing fine-scale functional impacts of drought beyond traditional methods. Vegetation physiological components explained most of the functional responses during drought, and physiological anomalies accounted for over 88% of total vegetation anomalies during drought peaks, highlighting their dominant role in early-stage drought response. What are the implications of the main findings? Physiological responses consistently outperform structural responses before, during, and after drought peaks, with intensified fluctuations at peak stress, underscoring vegetation's prioritization of rapid physiological adjustments. This study advocates for the integration of physiological remote sensing indicators to establish a more sensitive early warning system for drought. Spatial vulnerability patterns and quantified climate drivers directly support tailored water and climate adaptation strategies.Abstract African vegetation responses to extreme drought represent a key challenge for global change research and sustainable water-land resource management. Satellite remote sensing provides long-term observations of vegetation dynamics, yet conventional analyses focus on vegetation structural, greenness, or productivity changes, lacking of understanding on physiological adaptation. This study applies a multi-model framework integrating high-temporal-resolution (4-day) and multi-spectral satellite data with machine learning to disentangle structural and physiological responses across Central and Western Africa. Three key indicators were used: evapotranspiration (ET), relative solar-induced chlorophyll fluorescence (SIFrel), and the ratio of midday to midnight vegetation optical depth (VODratio), which respectively, represent water flux, photosynthetic activity, and water regulation. A random forest model, combined with SHapley Additive exPlanations (SHAP) analysis, was used to separate vegetation anomaly signals and identify key climatic controls. The results reveal pronounced differences in vegetation responses between arid and humid climatic regions. In arid regions, near-infrared reflectance of vegetation (NIRv) and solar-induced chlorophyll fluorescence (SIF) exhibited clear negative anomalies and significant pre-drought declines, accompanied by marked changes in vegetation optical depth (VOD), indicating canopy structural damage and reduced photosynthetic activity. In contrast, trend analysis revealed that although SIF and NIRv in humid regions showed relatively strong responses during the pre-drought phase, they did not exhibit significant trends after the drought peak, and changes in VOD were comparatively small, suggesting that higher water availability partially buffered the prolonged impacts of drought on vegetation structure and function. Process analysis showed that three months before and after drought peaks, physiological indicators exhibited strong anomalies that closely tracked drought duration. SIFrel, ET signals peaked earlier than water-content anomalies (VODratio), suggesting a two-phase regulation strategy: early stomatal closure followed by delayed deep-root water uptake. Physiological anomalies accounted for over 88% of total vegetation anomalies during drought peaks, highlighting their dominant role in early-stage drought response. Precipitation and temperature emerged as primary drivers, explaining 76.8% of photosynthetic variation, 60.3% of ET variation, and 53.9% of water-content variation in the development. The recovery is influenced by the duration of drought and the regrowth of vegetation. By explicitly decoupling physiological and structural vegetation responses, this study provides refined, process-based insights into African ecosystem adaptation to water stress. These findings contribute to more accurate drought monitoring, water availability assessment, and climate adaptation strategies, directly supporting sustainable water and land management goals.