Taking the Niutitang Shale in margin of Sichuan Basin as the target, we systematically studied the microscopic pore structures of the shale reservoir by using minerals composition analysis,Nitrogen Sorption-Desorption technology. Based on all of these, discussed the main factors to control the nanopore structure. The results revealed that, the micropores mainly consist of cylinder pores with two open ends, slit type pore with parallel plates. Pore diameters are in the range of 2-10nm with micropore predominant. In addition, organic carbon content is believed to be the major factors controlling the development of nanopores of the shale reservoirs and also the important substance to for the occurrence of shale gas.