The heterogeneity of shale is significant for the evaluation and "sweet spot" prediction of a shale gas reservoir. Core observations, thin sections, field emission scanning electron microscopy (FE-SEM), nitrogen gas adsorption (N(2)GA) and geochemical analyses were performed on shale samples from the Lower Longmaxi Formation in the Pengshui area of South China. In this study, the macroscopic and microscopic heterogeneities of the Longmaxi shale are revealed, and their origins and inner link are also discussed. The results show that three systems tracts were developed in the Lower Longmaxi Formation: a transgressive systems tract (TST), early highstand systems tract (EHST) and late highstand systems tract (LHST). From TST to LHST, TOC (total organic carbon), siliceous minerals (quartz + feldspar), and pyrite show an upward decreasing trend in weight content, while the clay minerals and carbonate contents increase upward. Hence, the TST, EHST and LHST shales are generally characterized by organic-rich shale lithofacies, organic-moderate shale lithofacies, and organic-lean shale lithofacies, respectively. The in situ gas content decreases from TST to LHST and primarily depends on TOC content. The sedimentary environment of the TST shale is an anoxic environment with high paleoproductivity, which then evolves to a dysoxic-oxic environment in the EHST shale and an oxic environment in the LHST shale with relatively low paleoproductivity. Organic matter pores are the primary contributors to the total pore volume in the TST shale, and then, the pore content and role in porosity decrease upward from EHST to LHST. However, the proportions of clay-related pores and brittle mineral-related pores gradually elevate from the TST shale to the LHST shale. The sedimentary environment, including water depth, redox conditions, paleoproductivity, terrigenous input and hydrodynamics, etc., control the development of organic matter, mineral composition, lithofacies association, color, bedding and palaeobios in the Lower Longmaxi shales, which constitute the macroscopic heterogeneity. Nevertheless, the microscopic heterogeneity of shale originates from diagenesis/catagenesis. Specifically, shales are primarily composed of interparticle pores and clay-related pores during deposition, and the porosity is reduced primarily under mechanical compaction and chemical cementation. As the burial depth and diagenetic degree increase, a large number of organic matter pores and dissolution pores begin to appear, which are associated with the hydrocarbon generation process. Moreover, macroscopic shale composition plays a crucial role in development levels of microscopic shale pores.