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South China Sea Operational Oceanography Forecasting System (SCSOFS) had been constructed and operated in National Marine Environmental Forecasting Center of China to provide daily updated hydrodynamic forecasting in SCS for the future 5 days since 2013. This paper presents recent comprehensive updates of the configurations of the physical model and data assimilation scheme in order to improve SCSOFS forecasting skills. It highlights three of the most sensitive updates, including sea surface atmospheric forcing method, tracers advection discrete scheme, and modification of data assimilation scheme. Inter-comparison and accuracy assessment among five versions during the whole upgrading processes are performed by employing OceanPredict Inter-comparison and Validation Task Team Class4 metrics. The results indicate that remarkable improvements have been achieved in SCSOFSv2 with respect to the original version known as SCSOFSv1. Domain averaged monthly mean root mean square errors decrease from 1.21 °C to 0.52 °C for sea surface temperature, from 21.6 cm to 8.5 cm for sea level anomaly, respectively. [ABSTRACT FROM AUTHOR]