An accurate 3D morphological analysis is critically needed to study the process–structure-property relationship in many application fields such as battery electrodes, fuel cells and porous materials for sensing and actuating. Here we present the application of a newly developed full field X-ray nano-scale transmission microscopy (TXM) imaging for a non-destructive, comprehensive 3D morphology analysis of a porous Ni–YSZ solid oxide fuel cell anode. A unique combination of improved 3D resolution and large analyzed volume (∼3600 μm3) yields structural data with excellent statistical accuracy. 3D morphological parameters quantified include phase volume fractions, surface and interfacial area densities, phase size distribution, directional connectivity, tortuosity, and electrochemically active triple phase boundary density. A prediction of electrochemical anode polarization resistance based on this microstructural data yielded good agreement with a measured anode resistance via electrochemical impedance spectroscopy. The Mclachlan model is used to estimate the anode electrical conductivity.