The prominent global warming event at the Paleocene-Eocene boundary (55 Ma), referred to as the Paleocene-Eocene Thermal Maximum (PETM), was characterized by rapid temperature increase and changes in the global carbon cycle in <10,000 yr, and a major extinction of benthic foraminifera. We explore potential causes of this extinction in response to environmental changes linked to a massive carbon injection by comparing sedimentary records with results from a comprehensive climate–carbon cycle model, and infer that an increase in oceanic vertical temperature gradients and stratification led to decreased productivity and oxygen depletion in the deep sea. Globally, productivity diminished particularly in the equatorial zone by weakening of the trades and hence upwelling, leading to a decline in food supply for benthic organisms. In contrast, near the Ross Sea, export of organic matter into the deep sea was enhanced due to increased near-surface mixing related to a positive salinity anomaly caused by a rise in wind-driven vertical mixing, contributing to the depletion of the deep-sea oxygen concentration, combined with a sluggish deep-sea circulation. The extinction of deep-sea benthic foraminifera at the PETM thus was probably caused by multiple environmental changes, including decreased carbonate saturation and ocean acidification, lowered oxygen levels, and a globally reduced food supply, all related to a massive carbon injection.