The Lower Silurian Longmaxi Formation in the southern Sichuan Basin is composed of a series of dark carbonaceous shales deposited in a hydrostatic shelf reduction environment. In this study, the ratio of uranium to thorium (U/Th), the total organic carbon (TOC), and the biological silicon content (SiBio) were selected as the characteristic parameters to precisely analyze the sedimentary environment and its impact on reservoir quality. The results show that the Weiyuan area in the Early Silurian Longmaxi period experienced two transgression-regression cycles, forming two third-class sequences, SSQ1 and SSQ2, which can be divided into six sedimentary microfacies: organic-rich siliceous argillaceous shelf, organic-rich silicon-containing argillaceous shelf, organic-rich silty argillaceous shelf, deep-water silty argillaceous shelf, shallow-water silty argillaceous shelf, and shallow-water argillaceous silty shelf microfacies. The organic-rich siliceous argillaceous shelf and organic-rich silicon-containing argillaceous shelf microfacies developed in the deepest transgressive system tract (TST1), with high U/Th, high TOC, and high SiBio, which are identified as the main control facies for reservoir development. These two microfacies are located in the middle of the study area, while a transition occurs in the east affected by the Neijiang Uplift. According to the classification criteria proposed in this article, the favourable shale gas reservoirs in Weiyuan area are characterized with high U/Th (>1.25), high TOC (>3%), and high SiBio (>15%). This paper proposed an evaluation method for shale sedimentary facies based on elemental and electrical logging characteristics, avoiding the limitations of core samples, which makes the quantitative division of shale sediments and the efficient recognition of high-quality reservoirs available. It is of great significance for delineating the potential production areas in the study area and beneficial for the scaled development of shale gas reservoirs.