AbstractMany countries have experienced the increase of groundwater depletion rate (GWDR), posing great challenges to the environment and society. Given the slow variation of groundwater, long‐term estimation of GWDR at high‐resolution is critical for sustainable managements of regional water resources and risks of hydrological extremes in a changing climate. However, limited in‐situ and satellite observations and uncertainties from hydrological model simulations prohibit reliable estimation of the long‐term trend and inter‐annual variation of GWDR. Using survey‐based water withdrawal and water availability datasets, this study provided a spatially distributed estimation of annual GWDR over China at the 0.25° × 0.25° grid scale for the period 1965–2016 using a flux‐based approach. The estimated GWDR has higher spatial resolution and longer temporal coverage than previous products. With the newly compiled data, we found that groundwater over China was depleted at an average rate of 20.4 km3 year−1 during 1965–2016, especially in the arid and semi‐arid areas of northern China. The GWDR showed a significant increasing trend during 1965–2016, but such trend slowed down from 0.66 km3 year−1 during 1965–2001 to 0.06 km3 year−1 during 2001–2016, which was mainly attributed to the deceleration in human water withdrawal. Further analysis showed that over 40% of the inter‐annual variability of GWDR could be explained by precipitation variability, and the climate control increased over time. This study suggested a growing control of climate variations on GWDR over China as the human water withdrawal has been decelerating, and a need for climate change adaptation for a sustainable groundwater management.