The Upper Ordovician Wufeng-Lower Silurian Longmaxi and the Lower Cambrian Qiongzhusi shales are the major targets for shale gas exploration and development in China. Although the two organic-rich shales share similar distribution ranges and thicknesses, they exhibit substantially different exploration and development results. This work analyzed the nanopore structures of the shale reservoirs in this region. Pore development of 51 shale samples collected from various formations and locations was compared using the petromineralogical, geochemical, structural geological and reservoir geological methods. The results indicate that the reservoir space in these shales is dominated by organic pores and the total pore volume of micropores, mesopores, macropores in different tectonic areas and formations show different trends with the increase of TOC. It is suggested that organic pores of shale can be well preserved in areas with simple structure and suitable preservation conditions, and the shale with smaller maximum ancient burial depth and later hydrocarbon-generation-end-time is also more conducive to pore preservation. Organic pore evolution models are established, and they are as follows: ① Organic matter pore development stage, ② Early stage of organic matter pore destruction, and ③ late stage of organic matter pore destruction. The areas conducive to pore development are favorable for shale gas development. Research results can effectively guide the optimization and evaluation of favorable areas of shale gas.