Model simulations of past climates are increasingly found to compare well with proxy data at a global scale, but regional discrepancies remain. A persistent issue in modeling past greenhouse climates has been the temperature difference between equatorial and (sub-)polar regions, which is typically much larger in simulations than proxy data suggest. Particularly in the Eocene, multiple temperature proxies suggest extreme warmth in the southwest Pacific Ocean, where model simulations consistently suggest temperate conditions. Here we present new global ocean model simulations at 0.1° horizontal resolution for the middle-late Eocene. The eddies in the high-resolution model affect poleward heat transport and local time-mean flow in critical regions compared to the non-eddying flow in the standard low-resolution simulations. As a result, the high-resolution simulations produce higher surface temperatures near Antarctica and lower surface temperatures near the equator compared to the low-resolution simulations, leading to better correspondence with proxy reconstructions. Crucially, the high-resolution simulations are also much more consistent with biogeographic patterns in endemic-Antarctic and low-latitude-derived plankton, and thus resolve the long-standing discrepancy of warm subpolar ocean temperatures and isolating polar gyre circulation. The results imply that strongly eddying model simulations are required to reconcile discrepancies between regional proxy data and models, and demonstrate the importance of accurate regional paleobathymetry for proxy-model comparisons.