Abstract The deposition and evolution of fine-grained sediments is a hot topic in fine-grained sedimentary rock studies and is important for accurately evaluating shale gas sweet spots. In this paper, the fine-grained deposition and evolution characteristics of the Wufeng-Longmaxi shales, major targets for Chinese shale gas exploration, were studied by using core observations, thin section analyses, scanning electron microscopy, geochemical analysis, and fossil identification. This work accurately identified six typical lithofacies; among them, the organic matter-rich siliceous shale facies (OMRSSF), the high-organic matter siliceous argillaceous shale facies (HOMSASF), and the medium-high organic matter low calcareous siliceous shale facies (M-HOMLCSASF) are favorable facies for shale gas exploration. The high-resolution isochronous unit in the shelf fine-grained sedimentary system was established, and the differential evolution of lithofacies in the system tract was discussed. The lithofacies deposition and differentiation in the transgressive system tract were controlled by the transgressive scale and tectonics under increasingly shallow water conditions. The lithofacies deposition and differentiation in the regressive system tract were controlled by tectonics and the preexisting lithofacies. The lithofacies in the regressive system tract had more frequent facies transitions and greater differentiation than those in the transgressive system tract, and they exhibited significant spatiotemporal inheritance. Sequential differential sedimentary sequences and symmetric differential sedimentary sequences were distinguished in the continental shelf sedimentary system. The lithofacies depocenters and subsidence centers were consistent in the transgressive system tract, while the tectonically active paleocontinent was important in the regression system tract. This study is of great significance for further high-resolution exploration of marine shale and improvement of the theory of shelf fine-grained sedimentary systems.