Shale contains a certain amount of natural fractures, which affects the mechanical properties of shale. In this paper, a bonded-particle model in particle flow code (PFC) is established to simulate the failure process of layered shale under Brazilian tests, under the complex relationship between layer plane and natural fracture. First, a shale model without natural fractures is verified against the experimental results. Then, a natural fracture is embedded in the shale model, where the outcomes indicate that the layer plane angle (marked as α) and the angle (marked as β) of embedded fracture prominently interfere the failure strength anisotropy and fracture pattern. Finally, sensitivity evaluations suggest that variable tensile/cohesion strength has a changeable influence on failure mechanism of shale, even for same α or/and β. To serve this work, the stimulated fractures are categorized into two patterns based on whether they relate to natural fracture or not. Meanwhile, four damage modes and the number of microcracks during the loading process are recognized quantitatively to study the mechanism of shale failure behavior. Considering the failure mechanism determines the outcome of hydraulic fracturing in shale, this work is supposed to provide a significant implication in theory for the engineering operation.