AbstractThe mesoscale eddies of which parameterization is needed in coarse‐resolution ocean models include not only the transient eddies akin to baroclinic instability but also the stationary eddies associated with topography. By applying a modified Lorenz‐type decomposition to the eddy‐permitting Southern Ocean State Estimate, we show that the stationary mesoscale eddies contribute a significant part to the total eddy kinetic energy, eddy enstrophy, and the total eddy‐induced isopycnal thickness and potential vorticity fluxes. We find that beneath middepth (about 1000 m) the upgradient eddy fluxes, or so‐called “negative” eddy diffusivities, are mainly attributed to the stationary mesoscale eddies, whereas the remaining transient eddy diffusivity is positive, for which the Gent and McWilliams (1990) parameterization scheme applies well. A quantitative method of measuring the anisotropy of eddy diffusivity is presented. The effect of stationary mesoscale eddies is one of major sources responsible for the anisotropy of eddy diffusivity. We suggest that an independent parameterization scheme for stationary mesoscale eddies may be needed for coarse‐resolution ocean models, although the transient eddies remain the predominant part of mesoscale eddies in the oceans.