Abstract Subduction of water masses is crucial for thermocline ventilation and climate variability. Using four ocean reanalysis products, we identify a significant interannual see‐saw variability in subduction rates of the South Pacific western and eastern Subtropical Mode Water (SPWSTMW and SPESTMW), which is primarily driven by changes in the mixed layer depth (MLD). Composite analysis demonstrates that the El Niño–Southern Oscillation induced winds are largely responsible for variations in latent heat flux, which alter MLD and modulate the subduction rates. In addition, a west‐strong/east‐weak subduction rate pattern in 1963–1978 and a west‐weak/east‐strong subduction rate pattern in 1998–2011 are observed. This long‐term shift can be attributed to shoaling MLD in the SPWSTMW formation region and intensifying wind stress curl in the SPESTMW formation region, both of which are associated with the intensification and southward extension of the subtropical high.