Characterizing past climate states is crucial for understanding the future consequences of ongoing greenhouse gas emissions. Here, we revisit the benchmark time series for deep ocean temperature across the past 65 million years using clumped isotope thermometry. Our temperature estimates from the deep Atlantic Ocean are overall much warmer compared with oxygen isotope-based reconstructions, highlighting the likely influence of changes in deep ocean pH and/or seawater oxygen isotope composition on classical oxygen isotope records of the Cenozoic. In addition, our data reveal previously unrecognized large swings in deep ocean temperature during early Eocene acute greenhouse warmth. Our results call for a reassessment of the Cenozoic history of ocean temperatures to achieve a more accurate understanding of the nature of climatic responses to tectonic events and variable greenhouse forcing.