This data accompanies Hess et al. (2026, Science Advances). It consists of Last Millennium (750 CE to present) surface-thermocline temperature differences from the Indonesian Seas, calculated from Mg/Ca-derived sea-surface temperatures (Globigerinoides ruber; Oppo et al., 2009, Esswein, 2012) and thermocline temperatures (Pulleniatina obliquiloculata; Hess et al., 2026). Temperatures derived using the species-specific calibrations of Hollstein et al. (2017). Data from cores recovered in very close proximity to each other have been grouped (Makassar Strait sites BJ8-03 31MC, 32GGC, 34GGC; and Java Sea Sites BJ8-03 6MC, 7GGC) and spliced; multicorer (MC) data were used for the period over which it is available. Ages have been updated to Marine20 and generated, with age uncertainty, using geoChronR (McKay et al., 2021).