Using observational temperature profiles, this study reveals that eddy-induced oceanic vertical temperature anomalies are geographically varying in the South China Sea (SCS). The maximum anomalies are more intensified in the central and south SCS. Due to ocean stratification, the eddy available potential energy (EAPE) can more comprehensively reflect the eddy effect on the ocean vertical structure. The EAPE within a composite eddy is the highest in the northern region and lowest in the southeastern region. The geographical variation of vertical anomalies induced by eddies is because of the combination effect of the ocean stratification, the background energy (available potential energy and barotropic kinetic energy), and the energy conversion rate. The anomalies induced by cyclonic and anticyclonic eddies might be asymmetrical in the same region. For example, in the regions to the west of Luzon Island and in the central west SCS, the temperature anomalies and EAPE within a composite cyclonic eddy are significantly larger than those within an anticyclonic eddy. This variation is owing to the different oceanic stratification along the tracks of cyclonic and anticyclonic eddies.