<p>Although the frequency and intensity of marine cold spell (MCS) events in the South China Sea have declined under global warming, their impacts on regional ocean environments and ecosystem processes remain substantial. This study examined how cyclonic mesoscale eddies (CEs) modulate the vertical structure of MCSs, using a combination of satellite observations, reanalysis datasets, and in situ temperature profiles based on data acquired from 1993 to 2022. Using the self-organizing map classification method, two typical vertical structures of MCS within CEs were identified: shallow MCSs, characterized by surface cooling that weakens with depth, and subsurface-intensified MCSs, featuring a pronounced cold anomaly peaking near the thermocline. The radial position of MCSs relative to an eddy center was found to be the dominant factor controlling the vertical cooling intensity—subsurface anomalies become more pronounced when an MCS occurs closer to the eddy core. Further analysis suggested that this subsurface cooling is primarily driven by an uplift of the thermocline associated with strong upwelling near the center of a CE. These findings reveal the important role of mesoscale eddy dynamics in shaping extreme cold events and will enhance our understanding of the subsurface extreme low temperatures associated with MCS events.</p>