Shale has a unique laminar structure that is currently the focus of considerable interest and a great deal of research in the academic community and industry. Studies have focused primarily on the differences among laminar combinations, whereas only a few have investigated the structure of individual lamina. In this study, we use typical organic-rich shale from the Cretaceous Nenjiang Formation in the Songliao Basin as an example and analyze each individual lamina of the shale on a millimeter scale. We have investigated heterogeneities among the different laminae by using X-ray fluorescence analysis, rock slicing, laser scanning confocal microscopy, field emission scanning electron microscopy, total organic carbon (TOC), rock pyrolysis, X-ray diffraction mineral analysis, electronic computer tomography (nano-CT), nitrogen adsorption, and other experimental methods. Four laminar units — composed of clay minerals, feldspar-quartz, and calcite — are distinguished based on their different levels of Ca, K, and Fe. We designate these units as UA, UB, UC, and UD (from the top to bottom in the formation). The palaeoenvironment, organic geochemical parameters, and mineral compositions of the different laminar structures are “two-stage” in character. From UD to UA, TOC values indicate a slightly decreasing trend, whereas the calcite content indicates a substantial increase, which is related to gradual reduction in the paleodepth, increasing aridity of the climate, increase of salinity, and decrease of reducibility during the sedimentary period. Different laminae correspond to different pore structures. The pore types in units UC and UD are mainly clay mineral-related pores and pyrite intergranular pores. In contrast, calcite dissolution pores are common in units UA and UB. Nitrogen adsorption and nano-CT data indicate that the pore development degree and pore size of organic matter in units UC and UD are better than those of units UA and UB. The porosity of UD is 2.6 times higher than that of UA. Laminae have an important influence on shale quality. The traditional approach to shale evaluation takes laminar combinations in shale strata as the research unit. Switching the focus to the heterogeneity of individual lamina could help in the selection of “sweet spots” and identification of optimal locations for shale oil exploration and development.