We aim to relate the morphology of the pore network of finely porous claystones to their fluid transport properties. By using Focused Ion Beam in combination with Scanning Electron Microscopy (FIB/SEM), we image the pore network of COx claystone from 2D image stacks and as 3D reconstructed volumes. Our FIB/SEM samples are representative of the mesoscopic matrix clay. Porosity resolvable by this technique is in the range 1.7–5.9% with peak pore sizes of 50–90 nm. 3D pore network skeletonization provides connected pore volumes between end surfaces, tortuosity, density, and shortest pore paths with their pore size distribution. At higher resolution, 2D transmission electron microscopy (TEM) reveals large amounts of smaller pores (2–20 nm) between clay aggregates, associated to a local porosity of 14–25%, and peak sizes of 4–6 nm. Liquid permeability predictions with Katz–Thompson model, at the FIB/SEM volume scale and at the TEM surface scale, are in good agreement with macroscopic measurements (on the order of 10−20 m2), showing that both mesopore sizes (peaks at 50–90 nm and 4–6 nm), located within the clay matrix, contribute to liquid transport.