In this study, in situ and assimilated model data are used to study spatiotemporal variation in eddy heat transport (EHT) in the South China Sea (SCS) and associated mechanisms. Combining satellite data with data from a mooring buoy deployed in the northwestern SCS, we find that surface EHT exhibits a direction opposite to that calculated by the frequently used downgradient method, indicating the existence of upgradient EHT in the SCS. A well-validated model further confirms this finding and gives a detailed distribution of EHT for the entire SCS. Both time-averaged zonal and meridional EHT are significant at southeast of Vietnam (SEV) and southwest of Taiwan (SWT), and their vertical structures suggest that most of the EHT is confined to the upper 400 m. It is found that the EHT is strong in summer, autumn, and winter but relatively weaker in spring, with the upper 30 m showing stronger EHT seasonality than the next 370 m. In terms of physical process, zonal EHT is associated with its barotropic term, whereas meridional EHT is determined by both the barotropic term and deviations in the baroclinic shear term. When using model data, the downgradient method fails to reproduce the model’s actual EHT. Instead, the model exhibits a significant upgradient region SWT and a significant downgradient region SEV. Possible reasons for these disparities are further investigated. The time-mean state of the baroclinic energy transfer tendency due to temperature is mainly controlled by barotropic processes, but its frequencies differ among its time-varying parts.