Abstract The present study combines palynological applications with advanced microscopic techniques to characterize the Utica, Haynesville and Fayetteville shale-gas source rocks. This unprecedented approach could offer an alternative way to measure the total organic carbon (TOC) content using the 2D subsurface Scanning Electron Microscope (SEM) images. This approach is considered to be a faster and inexpensive method compared to conventional geochemical analyses. Palynofacies analysis provided valuable information about kerogen type and its degree of thermal maturation, which are key parameters in shale-gas exploration. Moreover, it qualitatively allowed the estimation of important organic geochemical parameters such as vitrinite reflectance (Ro %) and numerical thermal alteration index (TAI). New high resolution microscopic solutions have successfully been exploited for source rock characterization at both micro- and nano-meter scales. In-situ Focused Ion Beam (FIB) and Scanning Electron Microscope (SEM) technologies provided new insights into rock fabrics such as porosity, permeability, tortuosity, anisotropy and kerogen content. Serial sectioning and sequential imaging using dual beam SEM/FIB instrument were implemented successfully to characterize the 2D kerogen content and 3D submicron-pore structures. Moreover, pores were found in organic matters with the size of nano level and occupy 40–50% of the kerogen body. A successful example of reconstructed 3D pore model from Fayetteville Shale is presented.