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Terrestrial water storage change (TWSC) plays a crucial role in the hydrological cycle and climate system. To date, methods including 1) the terrestrial water balance method (PER), 2) the combined atmospheric and terrestrial water balance method (AT), and 3) the summation method (SS) have been developed to estimate TWSC, but the accuracy of these methods has not been systematically compared. This paper compares the spatial and temporal differences of the TWSC estimates by the three methods comprehensively with the GRACE data during the 2002–13 period. To avoid the impact of different inputs in the comparison, three advanced reanalysis datasets are used, namely 1) the National Centers for Environmental Prediction (NCEP)–Department of Energy (DOE) Reanalysis II (NCEP R2), 2) the ECMWF interim reanalysis (ERA-Interim), and 3) the Japanese 55-Year Reanalysis (JRA-55). The results show that all estimates with PER and AT considerably overestimate the long-term mean on a regional scale because the data assimilation in the reanalysis opens the water budget. The difficulty of atmospheric observation and simulation in arid and polar tundra regions is the documented reason for the failure of the AT method to represent the TWSC phase over 30% of the region found in this study. Although the SS result exhibited the best overall agreement with GRACE, the amplitude of TWSC based on SS differed substantially from that of GRACE and the similarity coefficient of the global distribution between the SS-derived estimate and GRACE is still not high. More detailed considerations of groundwater and human activities, for example, irrigation and reservoir impoundments, can help SS to achieve a higher accuracy.