The vertically averaged temperature (TAV) from surface to 100 m depth of the South China Sea for the period 1959-1988 is analyzed. The results indicate that there is a significant long-term variability from interannual to interdecadal scales in the heat content in the upper ocean. The heat content of the upper ocean of the South China Sea increases evidently in the El Nino year. TAV anomaly in the ocean was negative from the end of 1950's to early 1970's, and then changed to positive. The changes of TAV of the ocean are closely related to ENSO events, the Asian winter monsoon and the tropical atmospheric circulation anomalies.