Using 29 years of expendable bathythermograph data, we studied the interannual temperature variability in the upper 300 m of the South China Sea (SCS). It is found that the temperature field has significant quasi-penta-annual variability throughout the 29 years. The interannual variability has a large decadal modulation. Although outside the SCS, in the Kuroshio, significant interannual variability extends to a much deeper layer beyond the 300 m depth, inside the SCS, especially in the central SCS, strong interannual variability is located near the 100 m depth and is capped by a surface layer of much weaker interannual variability. Similarities and differences in the temporal characteristics between the interannual variability inside and outside the SCS suggest that the interannual variability inside the SCS is primarily generated locally inside the SCS. In addition to the strong interannual variability, there exist strong decadal variability and a linear trend, which are also stronger in the subsurface than near the surface. It is found that below 100 m, the SCS has been cooling (linear trend) at a rate of ~0.4 ¿C per decade, decreasing from the eastern to the western basin. ¿ 1999 American Geophysical Union