In order to search after clay minerals of black shale and their effects on physical properties of shale gas reservoirs in the southeast of Chongqing, combination and distribution characteristic, formation mechanism and controlling factors of clay minerals and their effect on porosity and permeability are discussed in detail based on the knowledge of previous studies on clay minerals in petroliferous basins and taking Lujiao outcrop section in Pengshui County for an example. It has been discovered that type, quantity and distribution character of clay minerals are closely related to porosity and permeability of shale gas reservoirs.