A new observational dataset, the South China Sea Physical Oceanographic Dataset 2014, is examined to investigate the seasonal characteristics, formation mechanisms, and warming effects of the barrier layer (BL) in the South China Sea (SCS). Statistical analysis reveals that the BL is thicker and occurs more frequently during summer and early autumn, while in winter it often coexists with temperature inversions. The formation mechanisms are discussed from the perspective of the controlling regime and the net turbulent energy required for BL evolution. In the initial stage (March–May), the BL is absent due to weak mixing, scarce rainfall and surface warming. In the formation and maintenance stage (June–September), the BL grows in summer and persists into the transition season. The BLs can be classified into three regimes: the flux regime (in the Luzon Strait), the combined regime (in the eastern basin) and the wind regime (southeast of Vietnam). In the attenuation stage (October–February), associated with the winter monsoon, the BL mainly occurs in the combined regime (along the path of western boundary current) and the flux regime (in the southeast corner). The characteristics and generation mechanisms of the temperature inversions near the south Chinese coast, east of Vietnam, and in the Gulf of Thailand are also discussed. Our analysis further demonstrates that the BL has a significant warming effect on upper ocean temperature and heat content in the SCS.