The Paleocene-Eocene Thermal Maximum (PETM) has been held up as a past analog to future warm environments and presents the opportunity to study climate impacts on marine communities. Today the deep-sea benthic ecosystem contributes substantially to carbon cycling in seafloor sediments. During the PETM, organic rich and carbonate depleted sediments have been widely observed due to ocean acidification and reduced bottom water oxygenation. It is well known that deep-sea benthic foraminifers decreased their body-size and increased their metabolic rates, and food consumption in response to abruptly increasing temperature and changing surface water productivity. At DSDP Site 401, outer Bay of Biscay, North Atlantic, three species of marine adult ostracodes experienced a reduction in body-size in response to PETM warming. Using ostracode body size and benthic foraminifer chemistry as temperature proxies, we are able to assign changes in metabolic rate and organic carbon cycling of ostracodes. The ostracode body-sizes are positively correlated with benthic foraminiferal oxygen isotopes, indicating that the reduced body-sizes were caused by higher temperature during the PETM. Estimates of body size and temperature also suggest a decline in lifetime respiration in ostracode individuals during the PETM interval. The reduced respiration might be related to declining metabolic rates and oxidation of organic matters. Dwarfed ostracodes during the PETM core interval would uptake less organic matters than ostracodes in the pre-PETM interval, since ecological studies show that modern ostracode grazing rates depend on their body-sizes. Hence we consider major changes in the energy and carbon balance of the benthic food-chains and the reduction of organic carbon flux between the ostracodes and sediments during the PETM. The decline in ostracode carbon flux contrasts with previous interpretations that benthic foraminifers switched their taxonomic composition that recycled more organic matters.