Pore orientation in shale governs the fluid transport properties that are key to hydrocarbon production and potential CO₂ sequestration. The present work deals with the detailed study of nano-heterogeneities in shales, across the bedding plane, of varying thermal maturity and total organic carbon content using scanning small-angle X-ray scattering (SAXS) experiments. The complementary X-ray Micro-Computed Tomography (μCT) and functional group mapping elucidate the heterogeneity in micrometer resolution. 2D SAXS profiles of the shales show elliptical patterns indicating the nanoscale pore anisotropy in shale. The orientation of pores and their spatial variation is strongly dependent on the content of organic matter. The variance in the anisotropy parameter is validated with chemical mapping and high-resolution 3D imaging.