Strong eddy activities exist in the Leeuwin Current (LC) and the South Indian Countercurrent (SICC) systems. Through a detailed investigation based on satellite observations, we find a cyclonic preference for eddies with more frequent genesis, longer lifespan, smaller size and stronger intensity in both systems. The evolutions of amplitudes, radii and total vorticities of eddies can be classified as the generation, stable, and decay stages; however, those of the EKE and relative vorticities lack the stable stage, due to planetary vorticity changes related to the meridional deflections, as eddies drift westward. Eddy properties exhibit significant seasonal and interannual variations. In the LC system, more and stronger eddies tend to be generated in winter and in La Niña years; while in the SICC system, eddy properties generally reach their peaks in spring and in years when the negative Southern Annular Mode (SAM) occurs. And eddy intensities in the SICC system are also modulated by ENSO with about a one‐year phase lag. Through instability analysis, we find that baroclinic instability is the most dominant contributor to the development of eddies. By contrast, barotropic instability mainly acts to dampen eddies. Advection of EKE makes almost no net contribution when spatially averaged, although it is locally significant. Pressure work and dissipation may be nonnegligible EKE sinks in the LC system. The EKE variations in these two systems have close connections through the westward‐propagating baroclinic instability anomalies, which may explain the phase lags between these two systems.