The El Niño-Southern Oscillation (ENSO) has been classified into two types: the Central-Pacific (CP) type and the Eastern-Pacific (EP) type. To further understand the impacts of the two types of ENSO upon the thermal variability in the South China Sea (SCS), the reanalysis dataset dealing with the parameters of sea surface temperature (SST), surface air temperature, sea surface wind, precipitation, and sea-level pressure are analyzed herein via the regression-empirical orthogonal function. In addition, the Western Pacific Warm Pool (WPWP), the largest warm water mass in the world’s oceans, is known to have a strong impact upon the climate of its surrounding areas, including the SCS. Hence, the thermal variability and atmosphere-ocean interactions between the SCS and the WPWP during the CP and EP El Niño periods are also inspected in the present study. The results indicate that the SST anomalies significantly increase during the EP El Niño, but slightly decrease during the CP El Niño. In detail, a positive sea level pressure anomaly coupled with weaker northeasterly winds during the EP El Niño contribute to wet conditions, whereas a negative sea level pressure anomaly coupled with stronger northeasterly winds during the CP El Niño contribute to dry conditions. When multiple variables are compared, the EP El Niño is seen to have a more significant impact upon thermal variability than does the CP El Niño.

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