The 3D pore space and microglobule clustering network of polymer monolithic columns, which exhibited similar external porosity but significantly different chromatographic dispersion and permeability characteristics, were subjected to tomographic imaging followed by stereological analyses. The morphologies of the monolithic support structures were examined using serial-block-face scanning electron microscopy. The statistically computed characteristic chord-length, hydraulic radius and tortuosity of the pore are strongly associated to chromatographic transport processes, in particular, eddy dispersion and mass-transfer resistance contributing to chromatographic dispersion, and permeability of monolithic columns. Moreover, Giddings’ trans-column velocity bias has been quantified in monoliths for the first time. With demonstrated method robustness, the proposed morphological descriptors and the streamlined analysis workflow provide novel insights bridging the structure-performance relationship for future chromatography column design.