This study performs a comprehensive comparison of three key marine shale reservoirs in the southeastern margin of the Sichuan Basin, and explains why commercial gas production was only achieved in the Lower Silurian Longmaxi (LSL) and Upper Ordovician Wufeng (UOW) formations, but not in the Lower Cambrian Niutitang (LCN) formation. The experimental methods included in situ gas content and gas composition tests, methane adsorption analysis, low-pressure N2 adsorption, field emission scanning electron microscopy (FE-SEM), and total organic carbon (TOC) and vitrinite reflectance (Ro) analyses to evaluate the lithology, mineralogy, physical properties of the reservoir, organic geochemistry, in situ gas content and methane adsorption capacity characteristics of the three shales. The LCN shale has lower quartz and clay mineral contents and a low brittleness index, but higher contents of feldspar, pyrite and carbonate minerals than the LSL and UOW shales. The porosity and permeability of the LSL and UOW shales are higher than those of the LCN shale. The primary contributions to the high permeability in the LSL shale are its well-developed fractures and organic matter pores. In contrast, the over-mature LCN shale is unfavorable for the development of organic pores and fractures. Although the LCN shale has a higher methane sorption capacity than the LSL and UOW shales, the gas content and methane saturation of the LCN shale are distinctly lower than those of the LSL and UOW shales. This is primarily due to gas migration from the LCN shale, resulting from the activities of tectonic uplift and the unconformable contact between the LCN shale and the Dengying formation. When compared with gas shale in North America, the LSL shale is the most favorable shale reservoir out of the three Sichuan shales, while the combination of the LSL and UOW shales is also potentially productive. However, the individual single layer production of the UOW or LCN shales is still limited due to poor resource potential and/or reservoir physical characteristics in the study area.