Abstract: Taking the Lower Paleozoic marine shale in south China and the Carboniferous-Permian continental shale in North China as the research object, based on microscopic observations of field emission scanning electron microscope(FESEM) and related physical chemical testing, the comparative study on the mineral genesis, the maceral, organic pore and rock mechanical properties of shale is emphasized. The results show:there are differences and similarities between marine shale and continental shale. The basic feature of marine shale is that there are more authigenic minerals than terrigenous clast, the authigenic quartz is rich and homologous, differentiated and symbiotic with organic matter, the macerals are bituminite from lower organisms as raw materials, and nanoscale pores are well developed. The basic feature of continental shale is that there are mainly terrigenous clast and mud, less authigenic mineral content, the macerals are mainly organic clasts from higher plants as raw materials, and organic nanopores are not developed. These basic characteristics lead to significant differences in hydrocarbon generation potential, reservoir properties and fracturing properties of marine shale and continental shale. Shale gas resources evaluation and exploration and development need to be treated differently.