Abstract Widely developed in shale strata, laminae are the most typical shale sedimentary structure. To investigate their influence on shale gas reservoir quality, we conducted complementary studies by integrating microscopic observations, geochemical analyses, field-emission scanning electron microscopy (FE-SEM) imaging, and mercury intrusion capillary pressure (MICP) techniques. The microscopic observation of thin sections enabled us to detect the laminae characteristics, including the density and maximum thickness of individual lamina, and three types and stages of lamina development were identified. The total organic carbon (TOC) content, mineral composition, natural fracture, pore type, pore size distribution, porosity, permeability, and tortuosity were investigated in these different laminae types using FE-SEM, MICP and geochemical analysis. Combining the laminae characteristics and pore structure, we concluded that the organic pores and total pore area are mainly affected by the TOC content, whereas the development of the laminae controls the inorganic macropore scale and affects the pore size distribution. In addition, we found that the excessive development of shale laminae is not conducive to organic matter accumulation because of the change in redox condition, and because it has an adverse impact on the formation of complex artificial fractures during hydraulic fracturing.