<p>Intraseasonal variations of sea surface temperature (SST) in the South China Sea (SCS) during winter are investigated by using atmospheric and oceanic reanalysis in this study. The dominant pattern of SST variations within the 10–90-day timescale is derived by empirical orthogonal function analysis, which features a basin-wide warming or cooling spatial pattern, with a cycle period of 30–35 days. Composite analysis and mixed-layer heat budget analysis are conducted to investigate the physical process controlling SST variability. The formation of intraseasonal SST variations is primarily attributable to the forcing of wind-related latent heat flux and shortwave radiation flux changes. During the warming (cooling) period, anomalous southerly (northerly) winds tend to weaken (enhance) climatological northerly winds. This, in turn, results in a weakening (enhancement) of wind speed, favoring a reduction (increase) in latent heat flux from the ocean into atmosphere, accompanied by an increase (decrease) in shortwave radiation flux. In addition to surface heat flux forcings, ocean zonal advection is the second most significant contributing factor, exerting a negative effect. Finally, the effect of the Madden–Julian Oscillation (MJO) on the SST is studied. The variations in wind anomalies and surface heat flux changes associated with SST intraseasonal variability are significantly related to the MJO activities. The anomalous anticyclone (cyclone) in the northwest Pacific Ocean is induced by MJO, with enhanced (depressed) convection occurring in the Indian Ocean and depressed (enhanced) convection over the Maritime Continent and western Pacific Ocean, which accounts for the anomalous southerly (northerly) winds and enhanced (depressed) shortwave radiation observed.</p>