Climate change has been driving terrestrial water storage variations in the high mountains of Asia in the recent decades. This study is based on Gravity Recovery and Climate Experiment (GRACE) data to analyse spatial and temporal variations in terrestrial water storage (TWS) across the Tibetan Plateau (TP) from April 2002 to December 2016. Regional averaged TWS anomaly has increased by 0.20 mm/month (p < 0.01) during the 2002–2012 period, but decreased by − 0.68 mm/month (p < 0.01) since 2012. The seasonal variations in TWS anomalies also showed a decreasing trend from May 2012 to December 2016. TWS variations in the TP also showed significant spatial differences, which were decreasing in southern TP but increasing in the Inner TP. And a declining trend was clearly evident in the seasonal variability of TWS anomalies in the south TP (about − 30 to − 55 mm/a), but increasing in the inner TP (about 10–35 mm/a). Meanwhile, this study links temperature/precipitation changes, glacial retreat and lake area expansion to explain the spatial differences in TWS. Results indicated that precipitation increases and lake area expansion drove increasing TWS in the Inner TP during the 2002–2016 period, but temperature increases and glacial retreat drove decreasing TWS in southern TP.