Typical unconventional gas/liquid plays of China were studied using field-emission/focused ion beam scanning electron microscopy (SEM) for clay mineralogy and microstructural development. The SEM microstructural investigations of clay-rich shale and mudstone reservoirs provided significant information about clay mineral type, size, distribution and aggregates, which allows for interpretations regarding porosity preservation and petrophysical variability. The major clay-hosted porosity types are interparticle clay pores, intraparticle clay pores and aggregate pores. Interparticle clay pores occur in open spaces of the clay aggregates and include four subtypes: (1) elongated pores, (2) packed pores, (3) jagged pores and (4) card-house pores. Intraparticle clay pores are present within clay particles and have mostly secondary origin. These pores are diagenesis dependent and are restricted to secondary illite particles during the transformation of clay minerals from smectite to illite. Intraparticle clay pores constitute only isolated porosity and could not contribute to hydrocarbon molecule storage and migration. Aggregate pores were predominantly encountered in association with organic–clay and pyrite–clay aggregates. In places, organic–pyrite–clay aggregates can also display polymerization, but they do not contribute significantly to overall porosity and permeability. Combining SEM morphological analyses with the software ImageJ is critical in clay microstructure and porosity analyses via semi-quantitative characterization of the 3D pore surface, 2D pore profile, pore quantity, pore size, areal porosity, etc. These visual and semi-quantitative results highlight the significance of jagged pores and pyrite–clay aggregate pores in shale gas/liquid reservoirs because they may be important facilitators of gas storage and transmission.