Mesoscale eddies are quasi-circular ocean currents accompanied by dynamic and thermodynamic variations, and are classified as anticyclonic (AEs) and cyclonic eddies (CEs) according to their rotation direction. Eddies transition between surface cold CEs/surface warm AEs (“conventional” eddies) and surface warm CEs/surface cold AEs (“unconventional” eddies) during their lifetimes. However, the characteristics and mechanisms of these transitions remain unclear. In this study, satellite and in-situ data were used to explore the spatiotemporal variation and vertical structures of “conventional” and “unconventional” eddies during the evolution of long-lived eddies (>1 year) in the global ocean from 1993 to 2015. On average, long-lived eddies are “unconventional” for about 40% of their lifetimes, and these “unconventional” eddies are concentrated in the South Atlantic Ocean and off the western and southern coasts of Australia. “Unconventional” eddies show distinct temporal variation and subsurface temperature structures. Generally, cold AEs and warm CEs last <3 months and are more active in summer than in winter. They have cold or warm cores within the mixed layer depth of the water column, which is affected by eddy–wind interactions via eddy-induced Ekman pumping. However, some cold AEs in the South Atlantic and warm CEs in the South Indian Ocean can last for >3 months and display weak seasonal variation. In addition, their cold and warm cores can extend to ∼200 and ∼300 m, respectively, and are related to subduction and the Leeuwin Current System.