The organic carbon in shale has been proved to be a significant hydrocarbon source in two occurrences of discrete OM and organic-clay composites. Although the evolution of OM-hosted pores has been investigated by extensive research, the evolution of nanopores in discrete OM and organic-clay composites under additional stress is still unclear. In this study, two potential shales in China (Silurian Longmaxi (S(1)l) formation and Cambrian Niutitang (?(1)n) formation) were selected to examine the nanopores characteristics developed in discrete OM and organic-clay composites using field emission scanning electron microscopy (FE-SEM) and statistical analyses. The microstructure observations of the two shales show that during the growth of nanopores, the expansion of nanopores in composites was restricted by the narrow space between clay layers, and then, the nanopores would be protected from collapse or compaction by clay layers with further maturity. The discrete OM particles constantly suffer squeezing from brittle minerals and lead to the nanopores thrown into compressive environment, resulting in a preferred orientation along the edge of mineral particles and narrowing shape, as well as diminishing the pore sizes. For organic-clay composites, the development of nanopores is determined by additional stress state. Under compressive stress, no pores could be observed, while the nanopores are widely distributed in tensile environment or stress-free state. Consequently, the nanopores development in discrete OM and organic-clay composites are significantly affected by additional stress. The research findings imply the potential hydrocarbon source in the nanopores located in organic-clay composites and would bring inspiration for the exploitation of shale gas.