Drought is a critical hydrological challenge with ecological and socio-economic impacts, but its long-term variability and drivers remain insufficiently understood. This study proposes a deep learning-based framework to explore drought dynamics and their underlying drivers across China's major basins over the past four decades. The Long Short-Term Memory network was employed to reconstruct gaps in satellite-derived soil moisture (SM) datasets, achieving high accuracy (R2 = 0.928 and RMSE = 0.020 m3m-3). An advanced explainable artificial intelligence (XAI) approach was applied to unravel the mechanistic relationships between SM and critical hydrometeorological variables. Our results revealed a slight increasing trend in SM value across China's major basins over the past four decades, with a more pronounced downward trend in cropland that was more sensitive to water resource management. XAI results demonstrated distinct regional disparities: the northern arid regions displayed pronounced seasonality in drought dynamics, whereas the southern humid regions were less influenced by seasonal fluctuations. Surface solar radiation and air temperature were identified as the primary drivers of droughts in the Haihe, Yellow, Southwest, and Pearl River Basins, whereas precipitation is the dominant factor in the Middle and Lower Yangtze River Basins. Collectively, our study offers valuable insights for sustainable water resource management and land-use planning.