Sea level anomalies observed by altimeter during the 1993–2006 period, thermosteric sea level anomalies estimated by using subsurface temperature data produced by Ishii and SODA reanalysis data, tide gauge records and HOAPS freshwater flux data were analyzed to investigate the long term sea level change and the water mass balance in the South China Sea. The altimeter-observed sea level showed a rising rate of (3.5±0.9) mm yr-1 during the period 1993–2006, but this figure was considered to have been highly distorted by the relatively short time interval and the large inter-decadal variability, which apparently exists in both the thermosteric sea level and the observed sea level. Long term thermosteric sea level from 1945 to 2004 gave a rising rate of 0.15±0.06 mm yr-1. Tide gauge data revealed this discrepancy and the regional distributions of the sea-level trends. Both the ‘real’ and the thermosteric sea level showed a good correspondence to ENSO: decreasing during El Nio years and increasing during La Nia years. Amplitude and phase differences between the ‘real’ sea level and the thermosteic sea level were substantially revealed on both seasonal and interannual time scales. As one of the possible factors, the freshwater flux might play an important role in balancing the water mass. Sea level anomalies observed by altimeter during the 1993-2006 period, thermosteric sea level anomalies estimated by using subsurface temperature data produced by Ishii and SODA reanalysis data, tide gauge records and HOAPS freshwater flux data were analyzed to investigate the long term sea level change and the water mass balance in the South China Sea. The altimeter-observed sea level showed a rising rate of (3.5 ± 0.9) mm yr-1 during the period 1993-2006, but this figure was considered to have been highly distorted by the relatively short time interval and the large inter-decadal variability, which apparently exists in both the thermosteric sea level and the observed sea level. Long term thermosteric sea level from 1945 to 2004 gave a rising rate of 0.15 ± 0.06 mm yr-1. both the ’real’ and the thermosteric sea level showed a good correspondence to ENSO: decreasing during El Nio years and increasing during La Nia years. Amplitude and phase differences between the ’real’ sea level and the thermosteic sea level were substantially revealed on both seasonal and interannual time scales. As one of the possible factors, the freshwater flux might play an important role in balancing the water mass.