The late Miocene offers the opportunity to assess the sensitivity of the Earth's climate to orbital forcing and to changing boundary conditions, such as ice volume and greenhouse gas concentrations, on a warmer-than-modern Earth. Here we investigate the relationships between low- and high-latitude climate variability in an extended succession from the subtropical northwestern Pacific Ocean. Our high-resolution benthic isotope record in combination with paired mixed layer isotope and Mg/Ca-derived temperature data reveal that a long-term cooling trend was synchronous with intensification of the Asian winter monsoon and strengthening of the biological pump from ~7 Ma until ~5.5 Ma. The climate shift occurred at the end of a global δ13C decrease, suggesting that changes in the carbon cycle involving the terrestrial and deep ocean carbon reservoirs were instrumental in driving late Miocene climate cooling. The inception of cooler climate conditions culminated with ephemeral Northern Hemisphere glaciations between 6.0 and 5.5 Ma.