It is a great challenge for sedimentologists to perform the facies analysis of shales due to the lack of macro-structures and high heterogeneity in shale, and thus, conventional research methods are poorly applied in the field of shale sedimentology. To establish a typical depositional model for marine shales, a new method adopted from marine carbonate rocks was employed to perform the microfacies analysis of marine shales of the Wufeng and Longmaxi Formation in Sichuan Basin. This method emphasizes the fact that many skeletal constituents in marine shales have specific bathymetric distributions, allowing for a better understanding of the depositional process of shales. With this approach, a total of nine microfacies were identified and two depositional models for marine shales were proposed. The depositional models show that sea levels were high during the Middle to Late Wufeng period, which was followed by a rapid regression that led to a significant sea-level drop by over 50 m at the topmost of the Wufeng Formation, and consequently, widespread fine-grained sandy shales with large amounts of benthic bioclasts were deposited in the study region. The eustatic sea-level changes recovered by using the method of microfacies analysis are in line with the global trend, indicating that the method has promising applications in the field of marine shale sedimentology.