Ocean reanalysis provides a temporally continuous and spatially gridded four-dimensional estimate of the ocean state for a better understanding of the ocean dynamics and its spatial/temporal variability. Here we present a 19-year (1992-2010) high-resolution ocean reanalysis dataset of the upper ocean in the South China Sea (SCS) produced from an ocean data assimilation system. A wide variety of observations, including in-situ temperature/salinity profiles, ship-measured and satellite-derived sea surface temperatures, and sea surface height anomalies from satellite altimetry, are assimilated into the outputs of an ocean general circulation model using a multi-scale incremental three-dimensional variational data assimilation scheme, yielding a daily high-resolution reanalysis dataset of the SCS. Comparisons between the reanalysis and independent observations support the reliability of the dataset. The presented dataset provides the research community of the SCS an important data source for studying the thermodynamic processes of the ocean circulation and meso-scale features in the SCS, including their spatial and temporal variability.