Electron-beam physical vapor deposited (EB-PVD) thermal barrier coatings (TBCs) display a lower thermal conductivity compared with the deposited bulk material. This effect is achieved due to the presence of pores within these films. The spatial and geometrical characteristics of the porosity influence directly the magnitude of the achieved reduction of the thermal conductivity. In this work, three EB-PVD coating containing different microstructures were manufactured by varying the manufacturing process parameters during the deposition process. Their corresponding thermal conductivities were measured via the laser flash analysis method (LFA) in both the as-coated state and after ageing (1100 °C/100 h). Analysis of the pore formation during processing was carried out by ultrasmall-angle X-ray scattering (USAXS). This technique is supported with a computer based modeling developed by researchers at Advanced Photon Source (APS) in ANL, USA, and in National Institute of Standards and Technology (NIST), USA. The model enables the characterization of the size, shape, volume and orientation of each of the pore populations in EB-PVD TBCs. The effect of these spatial and geometrical characteristics of the porosity on the thermal conductivity of the EB-PVD coatings were studied via a non-interacting approximation based on Maxwell's model. Results of LFA measurements and the applied approximation indicate an interrelation between the microstructure and the thermal properties of the analyzed EB-PVD coatings. Microstructures containing a higher volume fraction of fine anisotropic intra-columnar pores, and larger voids between feather-arms oriented at lower angles toward the substrate plane correspond to lower thermal conductivity values. Inter-columnar gaps do no significantly contribute to lowering the thermal conductivity due to their orientation parallel to the heat flux and their lower volume fraction compared with the volume occupied by the primary columns. On heat treatment, the deepest section of the gaps between feather-arms break-up into arrays of nano-sized low aspect ratio voids. The anisotropic, elongated intra-columnar pores evolve toward low aspect ratio shapes that are less effective in reducing the thermal conductivity.