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Land subsidence mainly caused by excessive extraction of groundwater is a growing and worldwide problem. Sustained decline in groundwater level has a direct impact on land surface elevation. However, the impact may not be consistent across subsidence areas. The spatially varying relationship between land subsidence and groundwater level variations remains unclear. This study explores the spatio-temporal changes based on the observed data of groundwater levels and benchmark elevations from 2002 to 2009 in the Choshuichi alluvial fan of central Taiwan and examines the spatial heterogeneity with geographically weighted regression (GWR). The results reveal that the occurrence and development of land subsidence is closely related to the groundwater pumping. Moreover, the influence of groundwater level on land subsidence is more significant in the inland area. The study can help to predict the land subsidence caused by the overdraft of groundwater and provide an explicit strategy for groundwater resource management.