We propose a multifaceted isoneutral eddy transport diagnostic framework that combines the stationary-transient and Leonard’s decomposition in large eddy simulation (LES). We diagnose the subfilter flux, the isotropic transport coefficient, and the anisotropic transport tensor or eigenvalues in the Southern Ocean (SO). The anisotropic tensor greatly reduces the reconstruction error of the subfilter flux because of its ability to distinguish the directionality of dynamic information, especially the topographic effect. A thorough analysis of the anisotropic tensor or transport eigenvalues reveals that the sign combination of the transport eigenvalues of the symmetric tensor links to the evolution of domainintegral large-scale PV enstrophy and the combination of different signs is most often, meaning the dominance of filamentation process in the SO. In the region with intense anisotropy, the dominant eigenvector tends to be perpendicular to the large-scale PV gradient, indicating an important role of the PV barrier mechanism in the SO transport process. The two distinct decompositions leveraged in our framework generate intriguing and profound results. Under the stationary-transient decomposition, we find a significant stationary contribution and the duality of the topographic effect which can not only anchors stationary structures but also organizes transient motions. Leonard’s decomposition, allows us to investigate the collective effects of the standing wave train, cross-scale interaction, and subfilter eddy-eddy interaction on the filtered space-time scale. We emphasize the complete subgrid flux, not the mere Reynolds term, and the LES framework needs to be considered in the subgrid parameterization of the coarse resolution ocean model.