We present a Pulleniatina obliquiloculata Mg/Ca-derived thermocline water temperature record (TWT) covering the last 270,000 years at the south of the Lombok Strait, one of the main exits of the Indonesian Throughflow (ITF) into the Indian Ocean. The comparison with TWT records from the Java-Sumatra upwelling system and the Timor Sea suggests that changes in Lombok TWT reflect the balance between the wind-driven Java upwelling and the ITF thermocline transport. We show that the evolution of the TWT gradient (ΔTWT) between the upwelling site and the Lombok site can be used to decipher the relative strength of ITF through time. The 270 ka-long, ΔTWT record shows (i) that the ITF was weaker during MIS 6 and MIS 2–4 compared to the late Holocene, and was enhanced during MIS8, MIS 7, MIS 5 and the early Holocene, and that (ii) it varied with a strong precession-related component. Glacial-interglacial changes may reflect the modulation of ITF by sea-level changes through the modification of ITF pathways in the Indonesian Archipelago, and/or result from changes in the intensity of the Global Conveyor Belt. The strong precession contribution in the relative TWT strength at our Lombok site is interpreted as revealing the importance of southeast monsoon winds on ITF intensity.