China’s Yangtze and Yellow River Basins exhibit divergent drought patterns, yet the underlying mechanisms driving these differences remain underexplored. This study compares their drought characteristics from 1961 to 2022 using the Standardized Precipitation Index, Standardized Precipitation Evapotranspiration Index, and Palmer Drought Severity Index, and identifies their drivers through attribution models and interpretable machine learning. Our results reveal two distinct paradigms: the Yangtze Basin is characterized by high-frequency, over 14% in all seasons, short-duration droughts, reflecting a rapid hydrological response, while the Yellow River Basin experiences low-frequency, long-duration events indicative of strong soil moisture memory. Quantitative attribution demonstrates that atmospheric evaporative demand (VPD) plays a significantly greater role in the Yellow River Basin, contributing over 20% to soil drought, far exceeding its 14.4% contribution in the Yangtze Basin. Furthermore, their large-scale drivers differ fundamentally: the Yangtze Basin responds primarily to the Atlantic Multidecadal Oscillation (AMO) and Arctic Oscillation (AO), whereas the Yellow River Basin is mainly influenced by solar activity and the El Niño-Southern Oscillation (ENSO). These findings reveal that Yangtze drought is primarily driven by precipitation deficits, while Yellow River drought is a composite phenomenon amplified by evaporative demand. This distinction underscores the need for basin-specific water management strategies.