Understanding the impacts of climate extremes on the carbon cycle is important for quantifying the carbon-cycle climate feedback and highly relevant to climate change assessments. Climate extremes and fires can have severe regional effects, but a spatially explicit global impact assessment is still lacking. Here, we directly quantify spatiotemporal contiguous extreme anomalies in four global data sets of gross primary production (GPP) over the last 30 years. We find that positive and negative GPP extremes occurring on 7% of the spatiotemporal domain explain 78% of the global interannual variation in GPP and a significant fraction of variation in the net carbon flux. The largest thousand negative GPP extremes during 1982–2011 (4.3% of the data) account for a decrease in photosynthetic carbon uptake of about 3.5 Pg C yr−1, with most events being attributable to water scarcity. The results imply that it is essential to understand the nature and causes of extremes to understand current and future GPP variability.