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El Niño‐Southern Oscillation (ENSO) is the most dominant interannual signal of climate variability and profoundly affects river flooding globally, especially in East Asia. However, ENSO also has ∼2,000 and ∼1,000‐year cycles, but due to the lack of flood records with sufficient length, little is known about the ENSO's impact on floods at these millennial timescales. Here we test this in the middle‐lower Yangtze River by reconstructing the first Holocene flood record with optically stimulated luminescence and 14C ages of flood deposits. We find the periods with high flooding probability generally correspond with intervals of weakened solar activity. Importantly, the flood record displays 2,000 and 1,000‐year cycles similar to the ENSO record, and band‐pass filter results show the two records are synchronous at these bands. Our results reveal a persistent control of ENSO on millennial‐scale hydroclimatic variability in the Yangtze basin and likely other basins. Plain Language Summary: El Niño‐Southern Oscillation (ENSO) is the prominent pattern of interannual climate variability, profoundly affecting the river flow and flooding at the global scale. However, the ENSO's interannual cycle was strongly damped or even non‐existent in most of the Holocene, compared with a more robust millennial periodicity. It remains unclear whether a link exists between the flood and ENSO at millennial timescales due to the lack of sufficiently long flood series. Here we test this in the Yangtze River (YR) because ENSO has the most significant impact on this drainage area. We compiled the most detailed flood ages over the middle and lower YR to reconstruct the Holocene flood record. We found that the flood variations have prominent 2,000 and 1,000‐year cycles, and they exhibit in‐phase relationship with ENSO at these cycles, suggesting a persistent modulation of ENSO on the flooding at millennial timescales in the middle and lower Yangtze basin. This study contributes to a more comprehensive understanding of the driving forces of floods in the Yangtze catchment at millennial timescales, thereby aiding to accurately assess flood hazards and flooding prediction in hydroclimatic modeling for the densely populated Yangtze basin. Key Points: We reconstructed the Holocene flood record for the middle and lower Yangtze River by compiling optically stimulated luminescence and 14C ages of flood depositsThe flood record displays clear 2,000 and 1,000‐year cyclesThe flood record is synchronous with El Niño‐Southern Oscillation at 2,000 and 1,000‐year cycles [ABSTRACT FROM AUTHOR]