Abstract As a crucial component of global ocean circulation, the Indonesian Throughflow (ITF) is modulated by the El Niño‐Southern Oscillation. While multi‐year La Niña events often greatly enhance the volume transport of the ITF, the 2020–2023 La Niña caused only a modest increase in the ITF via Makassar Strait—0.3 Sv above the climatology of 12 Sv. Dominated by the 0–400 m velocity variations, the relatively weak transport is attributed to a milder Pacific easterly wind due to a weaker La Niña intensity. The strong negative Indian Ocean Dipole accompanying the third‐year La Niña induced the intensifying westerlies and anomalously elevated sea level over the eastern Indian Ocean during 2020–2023. Model experiments show that the Indian Ocean wind reduced the Pacific‐originated ITF inflow variability by 51% in 2020–2023. With the increasing frequency of multi‐year La Niña events, this study highlights the influence of Indian Ocean wind‐driven dynamics in modulating the ITF transport.