Abrupt climate changes such as Dansgaard–Oeschger (D-O) cycles and Heinrich events (HEs) are prevalent during the last glacial cycle and widely documented in Northern Hemisphere (NH) high latitudes. However, in tropical regions and the Southern Hemisphere (SH) far fewer records exist, especially in the western Pacific warm pool (WPWP) area. Here, we present a 50k archive of U37k′ sea surface temperature (SST), planktic foraminifera oxygen isotopes, and terrestrial input indicators including branched and isoprenoid tetraether (BIT) biomarkers, 232Th activity, and non-biogenic sediment components recorded in core MD052928 from the WPWP (near southern Papua New Guinea, PNG). The planktic foraminifer oxygen isotopes in the core show millennial-scale changes indicating fresher seawater during the NH cold periods (i.e., Heinrich Events, HEs) and suggesting hydrological changes that are most likely linked to the strength of the boreal winter Asian-Australian monsoon (AAM). Our observations are corroborated by evidence from the same core that indicates increased terrestrial input caused by higher precipitation on land and more river runoff from southern PNG during the cold periods. Consistent with other nearby hydrological records from land, our study indicates persistent millennial-scale hydrological changes within the past 50k in the western tropical Pacific and Southeast Asia. The timing of the millennial-scale changes appears to have been determined by the latitudinal displacement of the Intertropical Convergence Zone (ITCZ) that reflects a history of heat transport from the tropics and WPWP.