The Indonesian Throughflow (ITF) thermocline, as exclusive water source for the “warm water route” of the Atlantic Meridional Overturning Circulation (AMOC), provides waters that exit the Indian Ocean and join the AMOC upper limb via the Agulhas Leakage (AL). Hence, investigating long‐term variations in the ITF thermocline and its implications on the AL is important for understanding dynamics of the AMOC. Here, the thermohaline history of the ITF thermocline was reconstructed for the last ∼410 kyr based on δ18O and Mg/Ca of planktonic foraminifera from International Ocean Discovery Program Site U1483. By integrating the new and published records, we found that precession drives variation of the ITF thermocline through modulating the intensity of the Australian‐Indonesian winter monsoon, El Niño‐Southern Oscillation‐like states and formation of the North Pacific Tropical Water, in turn exerting a transoceanic influence on the amount of the AL and seawater temperature and salinity of the South Atlantic thermocline.