Nanoscale pore characteristics are crucial in assessing the resource potential of gas shales. Although the Niutitang formation was widely deposited in the upper Yantze Platform, South China and has been recognized as a promising shale gas reservoir, there lacks substantial breakthrough in the exploitation of shale gas from the Niutitang formation. Aiming at better understanding the reservoir properties and corresponding influential factors, 14 core samples from the Lower Cambrian Niutitang formation locating in the central Guizhou province were investigated in the current study to characterize the nanoscale pore system in the shale. Organic geochemical analyses (i.e., total organic carbon content and thermal maturity), X-ray diffraction, low pressure nitrogen adsorption, and field emission scanning electron microscopy were employed to obtain complementary information of the pore system. Measured TOC in this study is generally > 1.50% and averages 3.35%. All of the samples are in the over-maturity stage with R-o ranging from 2.39% to 3.29%. X-ray diffraction shows that quartz, clay minerals and plagioclase are the dominant minerals. Nitrogen adsorption results indicate that all of samples show type IIb nitrogen adsorption isotherms with type H3 hysteresis loops, which imply the coexistence of micropores, mesopores and macropores in the shale. The mesopores account for 60-70% of total pore volume, and are likely contributed by clay minerals and quartz. Organic matter appears to be the major contributor of the micropores and specific surface area, and is closely linked to the rapid decrease of average pore size with increasing burial depth. The field emission scanning electron microscopy reveals abundant organic matter pores in the middle-upper Niutitang formation, but lesser or smaller in the bottom of Niutitang formation. The lower Niutitang formation seems to develop substantial amounts of organic-clay aggregates, which preferentially lie parallel to the shale bedding and contain lots of nanoscale pores. The perpendicular variation of pore structure features is explained with multiple mechanisms, including thermal maturation of organic matter, compaction by strata pressure, dissipation of shale gas, etc. The results of our study have emphasized the interesting and complex features of the nanoscale pore structures in the gas shales, which may facilitate future assessment and exploitation of shale gas resources.