The water balance method PER（Precipitation-Evaporation-Runoff） combined with the land surface model VIC(Variable Infiltration Capacity) is used to estimate the temporal and spatial distribution of TWS (Terrestrial Water Storage) over the Yangtze River basin during 1982-2005. The TWSC (Terrestrial Water Storage Change) derived from PER method agrees well with that from GRACE (Gravity Recovery and Climate Experiment) observation, which indicates its reasonability. During the whole time period the mean annual temperature, precipitation, evapotranspiration, and runoff are 13.3 °C, 1036.8 mm, 459.4 mm, and 576.7 mm, respectively; the seasonal and annual variabilities of TWS are 23.3 mm and 37.0 mm respectively; the magnitude of TWSC is about 200 mm. For the three time periods 1982-1900 (control time), 1991-2000, and 2001-2005, the mean annual temperature is 13.0, 13.4, and 13.9 °C, and the mean annual precipitation is 1031.6, 1051.2, and 1017.4 mm, respectively; the corresponding mean annual evapotranspiration is 459.8, 459.9, and 457.7 mm, and the mean annual runoff is 569.0, 590.1, and 563.8 mm, respectively；the seasonal variability is 21.8, 26.8, and 22.9 mm, while the annual variability is 37.7, 29.8, and 17.6 mm; compared with 1982-1990, the warming rate during 2001-2005 is greater than that during 1991-2000; however, precipitation during 2001-2005 time period is reduced; while evapotranspiration changes a little during the three time periods and the runoff trend is similar to the precipitation trend. Compared with the control time period, basinintegrated TWS increased during 1991-2000 while decreased during 2001-2005. On the other hand, spatially TWS increased all over the basin apart from the middle and northwest of the region in comparison with control time period, and especially during 1991-2000 there is a distinct recharge of water in southeast while during 2001-2005 there is a great discharge in middle part of the basin, from which the authors inferred that the water resources of TWS in the southeast of the Yangtze River basin is abundant while that in middle and northwest of the whole basin is vulnerable and sensitive to climate change.