Groundwater recharge (GR) is a key component of regional and global water cycles and is a critical flux for water resource management. However, recharge estimates are difficult to obtain at regional scales due to the lack of an accurate measurement method. Here, we estimate GR using Gravity Recovery and Climate Experiment (GRACE) and Global Land Data Assimilation System (GLDAS) data. The regional-scale GR rate is calculated based on the groundwater storage fluctuation, which is, in turn, calculated from the difference between GRACE and root zone soil water storage from GLDAS data. We estimated GR in the Ordos Basin of the Chinese Loess Plateau from 2002 to 2012. There was no obvious long-term trend in GR, but the annual recharge varies greatly from 30.8 to 66.5 mm year−1, 42% of which can be explained by the variability in the annual precipitation. The average GR rate over the 11-year period from GRACE data was 48.3 mm year−1, which did not differ significantly from the long-term average recharge estimate of 39.9 mm year−1 from the environmental tracer methods and one-dimensional models. Moreover, the standard deviation of the 11-year average GR is 16.0 mm year−1, with a coefficient of variation (CV) of 33.1%, which is, in most cases, comparable to or smaller than estimates from other GR methods. The improved method could provide critically needed, regional-scale GR estimates for groundwater management and may eventually lead to a sustainable use of groundwater resources.