The GLORYS12v1 reanalysis data indicate the presence of a cyclonic eddy-like structure within the Kuroshio southwest of I-Lan Ridge, which tends to make the eddy-Kuroshio interactions more complex than previously understood. Consequently, it is crucial to investigate the morphological and energetic evolution of eddies during eddy-Kuroshio interactions in both the upper- and the lower-layer. The Helmholtz decomposition allows for the division of eddy kinetic energy into the parts associated with the enstrophy and strain energy. The pronounced variance in “energies” (enstrophy and strain energy) between early and later interaction phases in the upper-layer, as opposed to the less pronounced variance in the lower-layer, can be attributed to the formation of a vortex pair between the eddies’ lower-layer and the Kuroshio. Additionally, the relationship between eddy geometries and energetics is delineated using the multiple linear stepwise regression. Strain energy is identified as the primary driver of shape evolution in anticyclonic eddies, while both enstrophy and strain energy significantly influence the shape evolution of cyclonic eddies. Eventually, anticyclonic eddies transform into irregular structures by the western-flatting and eastern-curving, whereas cyclonic eddies evolve into irregular structures with the northern-flatting and southern-curving.