The Pacific intermediate water is essential for global ocean heat storage and transfer and connected to the higher latitude sea areas. Its thermohaline evolution and relationship to high latitudes on millennium scales, however, are both poorly understood. In this study, we used sediment core KX22–4 in the western equatorial Pacific to reconstruct the thermohaline and δ13C variations in the intermediate water over the past 28,000 years based on Mg/Ca, δ18O and δ13C measurements of deep dwelling planktonic foraminiferal species. The results show that during Heinrich Stadial 1, the temperature of intermediate water rapidly increased by roughly 6 °C and was simultaneous with the Southern Ocean surface water, carrying a typical Antarctic signature along with the salter and reduced δ13C signals. The Southern Hemisphere climatic development and the advection of the thermal anomaly into the tropical intermediate Pacific via the Southern Ocean intermediate water are thought to be closely coupled.