The Yangtze River Basin (YRB), home to around 400 million people, boasts of abundant water resources and significant spatial heterogeneity. Revealing the driving factors of water storage changes in YRB is essential for effective water resource management and sustainable development. In this study, we assess the drivers of total water storage (TWS) changes derived from the Gravity Recovery and Climate Experiment (GRACE) satellite within YRB from two perspectives: water balance and water storage components, including snow water equivalent (SWE), surface water storage (SWS), soil moisture storage (SMS), and groundwater storage (GWS). We also investigate the influence of reservoirs (e.g., Three Gorges Reservoir (TGR)), lakes (e.g., Dongting, Poyang, and Taihu), and glacier thawing on regional TWS changes. The results reveal an apparent increasing trend in YRB’s TWS from 2002 to 2022, while trends in precipitation, evapotranspiration, and runoff do not adequately account for this observed trend. In addition, our findings show that the increased TWS primarily occurs during the non-monsoon season, characterized by limited precipitation. The analysis of water components shows that the rise in TWS within YRB is predominantly attributed to GWS accumulation. SWS also contributes to the increasing TWS, primarily driven by the reservoir filling. The filling of TGR explains the observed TWS increase in Hubei province, whereas Lake Poyang accounts for about 30% of the positive TWS trend in Jiangxi province. Our comprehensive analysis systematically unveils the drivers of water storage changes in YRB, providing valuable insights for its sustainable water resource management and utilization.