Changning and Fuling are two of the best-known shale gas fields in China, located at two different depositional centers of the Upper Ordovician Wufeng Formation to the lower Silurian Longmaxi Formation in the Sichuan Basin. However, there are significant differences in the gas content of the Wufeng-Longmaxi shales between these two areas, despite their similar average total organic carbon contents and thickness. To elucidate the main factors responsible for the differences in the shale gas content between Changning and Fuling, two shallow wells were drilled to investigate their mineralogical and petrophysical properties as well as the organic matter–associated pore structure of the Wufeng-Longmaxi shales. A comparison of these reservoir properties was also made with those of the Jiaoye 4 well from the Fuling shale gas field. Because the Wufeng-Longmaxi shales in these two areas were deposited within different sedimentary environments and experienced different tectonic intensities, the present study focused mainly on investigating whether and how these differences have affected the petrophysical properties of the shale interval. The results indicated that intensive carbonate cementation in Changning significantly reduced the total pore volume and total specific surface area of the shale interval, and thus degraded the reservoir connectivity. However, compared with the Fuling field, a relatively weak tectonic compaction deformation in the Changning field was beneficial to the preservation of pore volume. Therefore, more intensive carbonate cementation may have been one critical geological factor responsible for the lower gas content in the Wufeng-Longmaxi shale reservoirs in the southern Sichuan Basin.