Ocean-atmosphere interactions in the tropical Pacific region have a strong influence on global heat and water vapour transport and thus constitute an important component of the climate system. Changes in sea surface temperatures and convection in the tropical Indo-Pacific region are thought to be responsible for the interannual to decadal climate variability observed in extra-tropical regions, but the role of the tropics in climate changes on millennial and orbital timescales is less clear. Here we analyse oxygen isotopes and Mg/Ca ratios of foraminiferal shells from the Makassar strait in the heart of the Indo-Pacific warm pool, to obtain synchronous estimates of sea surface temperatures and ice volume. We find that sea surface temperatures increased by 3.5-4.0 degrees C during the last two glacial-interglacial transitions, synchronous with the global increase in atmospheric CO2 and Antarctic warming, but the temperature increase occurred 2,000-3,000 years before the Northern Hemisphere ice sheets melted. Our observations suggest that the tropical Pacific region plays an important role in driving glacial-interglacial cycles, possibly through a system similar to how El Niño/Southern Oscillation regulates the poleward flux of heat and water vapour.