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Terrestrial gross primary production (GPP) is the basis of vegetation growth and food production globally and plays a critical role in regulating atmospheric CO2 through its impact on ecosystem carbon balance. Even though higher CO2 concentrations in future decades can increase GPP, low soil water availability, heat stress and disturbances associated with droughts could reduce the benefits of such CO2 fertilization. Here we analysed outputs of 13 Earth system models to show an increasingly stronger impact on GPP by extreme droughts than by mild and moderate droughts over the twenty-first century. Due to a dramatic increase in the frequency of extreme droughts, the magnitude of globally averaged reductions in GPP associated with extreme droughts was projected to be nearly tripled by the last quarter of this century (2075-2099) relative to that of the historical period (1850-1999) under both high and intermediate GHG emission scenarios. By contrast, the magnitude of GPP reductions associated with mild and moderate droughts was not projected to increase substantially. Our analysis indicates a high risk of extreme droughts to the global carbon cycle with atmospheric warming; however, this risk can be potentially mitigated by positive anomalies of GPP associated with favourable environmental conditions.