The water resources crisis is intensifying in Southwest China (SWC), which includes the world’s largest continuous coverage of karst landforms, due to recent severe drought events. However, because of the special properties of karstic water system, such as strong heterogeneity, monitoring the variation of karstic water resources at large scales remains still difficult. Satellite gravimetry has emerged as an effective tool for investigating the global and regional water cycles. In this study, we used GRACE (Gravity Recovery and Climate Experiment) data from January 2003 to January 2013 to investigate karstic water storage variability over the karst region of SWC. We assessed the impacts of the recent severe droughts on karst water resources, including two heavy droughts in September 2010 to May 2010 and August 2011 to January 2012. Results show a slightly water increase tend during the studied period, but these two severe droughts have resulted in significant water depletion in the studied karst region. The latter drought during 2011 and 2012 caused more water deficits than that of the drought in 2010. Strong correlation between the variations of GRACE-based total water storage and precipitation suggests that climate change is the main driving force for the significant water absent over the studied karst region. As the world’s largest continuous coverage karst aquifer, the karst region of SWC offers an example of GRACE applications to a karst system incisively and will benefit for water management from a long-term perspective in karst systems throughout the world.