Abstract: The difference in microstructure leads to the diversity of shale mechanical properties and bedding fractures distribution patterns. In this paper, the microstructure and mechanical properties of Longmaxi marine shale and Qingshankou continental shale were studied by X-ray diffractometer (XRD), field emission scanning electron microscope (FE-SEM) with mineral analysis system, and nanoindentation. Additionally, the typical bedding layers area was properly stratified using Focused Ion Beam (FIB), and the effects of microstructure and mechanical properties on the distribution patterns of bedding fractures were analyzed. The results show that the Longmaxi marine shale sample contains more clay mineral grains, while the Qingshankou continental shale sample contains more hard brittle mineral grains such as feldspar. For Longmaxi marine shale sample, hard brittle minerals with grain sizes larger than 20 μm is 18.24% and those with grain sizes smaller than 20 μm is 16.22%. For Qingshankou continental shale sample, hard brittle minerals with grain sizes larger than 20 μm is 40.7% and those with grain sizes smaller than 20 μm is 11.82%. In comparison to the Qingshankou continental shale sample, the Longmaxi marine shale sample has a lower modulus, hardness, and heterogeneity. Laminated shales are formed by alternating coarse-grained and fine-grained layers during deposition. The average single-layer thickness of Longmaxi marine shale sample is greater than Qingshankou continental shale sample. The two types of shale have similar bedding fractures distribution patterns and fractures tend to occur in the transition zone from coarse-grained to fine-grained deposition. The orientation of the fracture is usually parallel to the bedding plane and detour occurs in the presence of hard brittle grains. The fracture distribution density of the Longmaxi marine shale sample is lower than that of the Qingshankou continental shale sample due to the strong heterogeneity of the Qingshankou continental shale. The current research provides guidelines for the effective development of shale reservoirs in various sedimentary environments.