Abstract: Based on the identification and genetic analysis of the Lower Paleozoic marine shale in the Southern China, the genetic types of mineral pores and their influence on the physical properties of shale reservoir are studied in detail. According to the microstructure morphology of pores under the field emission scanning electron microscope (FESEM), and the mineral composition, sedimentation, diagenesis, tectonic of shale are also synthetically considered, the morphology-origin of mineral pores in Lower Paleozoic marine shale reservoir in Southern China are divided into three types:1) main pores(bedding gap, mud pores, gaps between ingredient and interbedding fissure), common and numerous under microscope, have a certain influence on the properties of shale reservoir; 2) other pores(intercystalline pores, corroded pores, gas-liquid inclusion pores and gaps between pieces), rare and limited in the shale, have little influence on the properties of shale reservoir; 3) tectonic pores(tectonic fissure and particle pores) is the record of geological tectonic activity, plaid the role of double-edged sword for the shale reservoir. Main pore types are different in different shale lithology, different pores have different effects for shale reservoir.