Abstract A pore is an essential component of shale gas reservoirs. Clay minerals are the adsorption carrier second only to organic matter. This paper uses the organic maturity test, Field-Emission Scanning Electron Microscopy (FE-SEM), and X-ray Diffraction (XRD) to study the structure and effect of clay minerals on storing gas in shales. Results show the depositional environment and organic maturity influence the content and types of clay minerals as well as their structure in the three types of sedimentary facies in China. Clay minerals develop multi-size pores which shrink to micro- and nano-size by close compaction during diagenesis. Micro- and nano-pores can be divided into six types: 1) interlayer, 2) intergranular, 3) pore and fracture in contact with organic matter, 4) pore and fracture in contact with other types of minerals, 5) dissolved and, 6) micro-cracks. The contribution of clay minerals to the presence of pores in shale is evident and the clay plane porosity can even reach 16%, close to the contribution of organic matter. The amount of clay minerals and pores displays a positive correlation. Clay minerals possess a strong adsorption which is affected by moisture and reservoir maturity. Different pore levels of clay minerals are mutually arranged, thus essentially producing distinct reservoir adsorption effects. Understanding the structural characteristics of micro- and nano-pores in clay minerals can provide a tool for the exploration and development of shale gas reservoirs.