Surface-intensified and subsurface-intensified eddies are two types of mesoscale eddies with distinct vertical structures, suggesting that they may play different roles in oceanic transport. However, our understanding of their structure and transport characteristics in the Southeastern Indian Ocean (SEIO) remains insufficient. Utilizing GLORYS12V1 reanalysis data, this study investigates the three-dimensional structure of eddies in the SEIO. We find that subsurface-intensified eddies occur more frequently at higher latitudes and exhibit longer lifespans with pronounced meridional displacements. Their surface temperature and salinity anomalies commonly display a dipole structure, whereas those of surface-intensified eddies are mainly monopolar. Estimates of eddy-induced transport indicate that surface-intensified anticyclonic eddies and subsurface-intensified cyclonic eddies are the major contributors to the meridional eddy-induced heat transport in the SEIO. The 10-year mean transports show that surface-intensified anticyclonic eddies dominate the poleward heat transport at lower latitudes, reaching ~17 TW near 27°S, whereas subsurface-intensified cyclonic eddies dominate the equatorward transport at higher latitudes, reaching ~16 TW near 42°S. This high-latitude equatorward transport deviates from the expectation of gradient diffusion theory. An asymmetry decomposition further reveals that eddy velocity, tracer, and shape asymmetries substantially contribute to the direction and magnitude of net transport, highlighting the need to incorporate eddy vertical structure and internal asymmetry into parameterizations of eddy-induced transport.