Abstract Reanalysis data reveals that the South China Sea (SCS) experiences intensified subsurface marine heatwaves (MHWs) and marine cold spells (MCSs) near the thermocline. On the interannual scale, surface and subsurface events demonstrate an opposite correlation with ENSO, primarily due to distinct drivers at different depths. During the developing phase of El Niño, the Luzon Strait transport, indicative of the SCS throughflow (SCSTF), increases and necessitates stronger upwelling for mass balance. This upwelling, acting on large subsurface vertical temperature gradients, induces significant subsurface cooling and the occurrence of MCSs. As El Niño matures, excessive atmospheric heat flux warms the surface layer, triggering surface MHWs. This heat is then transported downward mainly by vertical turbulent mixing, diminishing subsurface cooling, and terminating subsurface MCSs. The scenario reverses during La Niña events. The SCSTF serves as a vital oceanic pathway, transmitting ENSO signals into the SCS and profoundly modulating subsurface MHWs and MCSs.

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