Abstract: The water storage variation in Heihe River basin is very important to the ecological environment and economic construction. Based on a hybrid filtering scheme of the decorrelated filter P3M6 and 300km Gaussian filter, the terrestrial water storage variations in Heihe River basin are recovered from the GRACE (Gravity Recovery and Climate Experiment) temporal gravity field models GRGS-EIGEN-GL04 for the period from April 2004 until June 2011. By removing the soil moisture and snow mass changes derived from the global hydrological model GLDAS (Global Land Data Assimilation System), the groundwater storage variations in space-time domain are obtained in Heihe river basin, and preliminarily confirmed by the groundwater observations from 23 monitoring wells in Zhangye city. Two conclusions can be drawn from the results: (1) the terrestrial water storage variations tend to reduce with the average rate of 2.3cm/a in terms of equivalent water height (EWH), consistent with the regional climate changes and the results from the global hydrological mode CPC (Climate Prediction Center). (2) The groundwater storage variations show the same tendency at the average loss rate of 2.5cm/a EWH. While the regional groundwater storage rates are different, the average loss rates in upstream and midstream areas are almost the same, but obviously larger than that of downstream area of Heihe River Basin.