Abstract: Based on the META3.2 DT mesoscale eddy trajectory data and the ARMOR3D temperature, salinity, and current data, the statistical characteristics and three-dimensional structures of cyclonic and anticyclonic eddies with radii exceeding 50 km in the sea south of Japan (131°-142°E, 28°-35°N, the study region) during 1993-2021 were systematically analyzed. The results show that the mean daily numbers of cyclonic and anticyclonic eddies in the study region are 3.6 and 2.8, respectively. Approximately 75% of cyclonic eddies have radii between 50 and 110 km and amplitudes ranging from 0 to 25 cm, while about 75% of anticyclonic eddies have radii between 50 and 130 km and amplitudes between 0 and 20 cm. Around 75% of both cyclonic and anticyclonic eddies have lifetimes shorter than 40 days. In the open ocean of the southern part of the study region, both cyclonic and anticyclonic eddies predominantly propagate westward. In contrast, within the Kuroshio and its northern flank, most cyclonic eddies propagate eastward, while within the southern flank of the Kuroshio, some anticyclonic eddies also exhibit eastward propagation. Cyclonic eddies frequently occur in the northern flank of the Kuroshio in the area centered at 137°30′E and 33°30′N. This is mainly attributed to barotropic instability, baroclinic instability, and the input of positive vorticity from the Kuroshio. Meanwhile, anticyclonic eddies frequently appear in the southern flank of the Kuroshio in the area centered at 136°00′E and 31°30′N. This is primarily caused by baroclinic instability and the input of negative vorticity from the Kuroshio. Vertically, the influence of cyclonic eddies penetrates over 1,200 m, whereas that of anticyclonic eddies is approximately 1 000 m. Both types of eddies exhibit subsurface-intensified structures, with the maximum temperature and salinity anomalies induced appearing at a depth of about 400 m. In addition, neither cyclonic nor anticyclonic eddies show obvious vertical tilting. This study enhances our understanding of the statistical characteristics and three-dimensional structures of mesoscale eddies in the sea south of Japan, providing a solid foundation for further investigations into eddy–Kuroshio interactions. It also serves as a scientific reference for China’s navigational safety and marine environment forecasting in relevant maritime regions.