In this study, Sea surface temperature (SST) derived from National Oceanic and Atmospheric Administration (NOAA) series satellites Advanced very high resolution radiometer (AVHRR) infrared radiometer and sea surface height (SSH) derived from TOPEX/Poseidon satellite altimeter were used to estimate the sea surface heat storage in the South China Sea (SCS). Temperature profiles from in-situ measurements are used to integrate the heat storage of water column and estimate the error of heat storage derived from satellite data. The empirical orthogonal function (EOF) method was applied to analyze the variation of heat storage of SCS. The results show that the heat storage in SCS increases from 1993 to 2001 and decreases slowly from 2001 to 2004. Furthermore, there are two dynamical instability areas appearing in SCS. The dynamical instability area west off Luzon Island has a similar heat storage variation to the whole SCS. However, at the dynamical instability area of offshore of central Vietnam coast, the heat storage increases from 1993 to 2001, but decreases rapidly from 2001 to 2004. The variation of surface heat storage is also affected by ENSO events. The surface heat storage increases during El Niño events and decreases during La Niña events.