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Dynamics driving the El Niño–Southern Oscillation (ENSO) over longer-than-interannual time scales are poorly understood. Here, we compile thermocline temperature records of the Indo-Pacific warm pool over the past 25,000 years, which reveal a major warming in the Early Holocene and a secondary warming in the Middle Holocene. We suggest that the first thermocline warming corresponds to heat transport of southern Pacific shallow overturning circulation driven by June (austral winter) insolation maximum. The second thermocline warming follows equatorial September insolation maximum, which may have caused a steeper west-east upper-ocean thermal gradient and an intensified Walker circulation in the equatorial Pacific. We propose that the warm pool thermocline warming ultimately reduced the interannual ENSO activity in the Early to Middle Holocene. Thus, a substantially increased oceanic heat content of the warm pool, acting as a negative feedback for ENSO in the past, may play its role in the ongoing global warming.