Interannual variability of eddy kinetic energy (EKE) in the subtropical southeast Indian Ocean (SEIO) is investigated using satellite observations in three regions in the 20 degrees S-35 degrees S latitude band: R1 (108 degrees E-115 degrees E), R2 (100 degrees E-108 degrees E), and R3 (60 degrees E-100 degrees E). The El Nino-Southern Oscillation (ENSO) plays an important role in modulating the interannual variability of EKE in the SEIO. EKE in the three regions shows negative correlations with the Nino3.4, lagging Nino3.4 by 2, 14, and 22 months, respectively. In R1, the ENSO modulates the interannual variability of EKE through influencing baroclinic instability of meridional velocity shear between the upper poleward Leeuwin Current (LC) and the underlying equatorward Leeuwin Undercurrent (LUC). During La Nina (El Nino) year, both the poleward LC and equatorward LUC strengthened (weakened) due to the high (low) sea level anomaly (SLA) propagating from the Pacific Ocean as Rossby wave under geostrophic equilibrium, and baroclinic instability of vertical shear enhanced (slackened), further induced the strong (weak) EKE in the eastern boundary. In R2, the ENSO modulates the interannual variability of EKE through influencing baroclinic instability of zonal velocity shear between the central and southern branches of the upper eastward South Indian Countercurrent (SICC) and the lower extending westward South Equatorial Current (SEC). In R3, both the ENSO and the Southern Annual Mode modulate the interannual variability of EKE through influencing baroclinic instability of zonal velocity shear between the SICC and SEC. The interannual variability of EKE in the interior SEIO could be influenced by westward propagation of EKE originated from eastern boundary.