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In this study, the water balance-based Precipitation-Evapotranspiration-Runoff (PER) method combined with the land surface model Variable Infiltration Capacity (VIC) was used to estimate the spatiotemporal variations of terrestrial water storage (TWS) for two periods, 1982-2005 (baseline) and 2071-2100, under future climate scenarios A2 and B2 in the Yangtze River basin. The results show that the estimated TWS during the base-line period and under the two future climate scenarios have similar seasonal amplitudes of 60-70 mm. The higher values of TWS appear in June during the baseline period and under the B2 scenario, whereas the TWS under A2 shows two peaks in response to the related precipitation pattern. It also shows that the TWS is recharged from February to June during the baseline period, but it is replenished from March to June under the A2 and B2 scenarios. An analysis of the standard derivation of seasonal and interannual TWS time series under the three scenarios demonstrates that the seasonal TWS of the southeastern part of the Yangtze River basin varies remarkably and that the southeastern and central parts of the basin have higher variations in interannual TWS. With respect to the first mode of the Empirical Orthogonal Function (EOF), the inverse-phase change in seasonal TWS mainly appears across the Guizhou-Sichuan-Shaanxi belt, and the entire basin generally represents a synchronous change in inter-annual TWS. As a whole, the TWS under A2 presents a larger seasonal variation whereas that under B2 displays a greater interannual variation. These results imply that climate change could trigger severe disasters in the southeastern and central parts of the basin.