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As the waters of marine primary production, the euphotic zone is the primary living environment for aquatic organisms. Eddies account for 90% of the ocean’s kinetic energy and they affect marine organisms’ habitats by the excitation of vertical velocities and the horizontal advection of nutrients and ecosystems. Satellite observations indicate that anticyclones mainly deepen the euphotic zone depth, while cyclones do the opposite. The anomalies reach 5 m on average in the region of high eddy amplitude and frequent eddy occurrence. In addition, we found that the anomalies have an extreme value in each of the 5°–23° and 23°–55° and reach a maximum at around 38 degrees with the increase in latitude. In the eddy-center coordinate system, the minus gradient direction of the negative anomaly is consistent with the background flow field and the direction of the eddy movement. Meanwhile, the anomaly increases along the radial direction to about 0.2r and then decreases. Finally, there is a significant linear correlation between the anomaly magnitude and the eddy amplitude. The conclusion of this research and related mechanism explanation contributes to marine biology research and conservation, the estimates of marine primary productivity, and the understanding of the biogeochemical properties of eddy modulation in the upper water column.