The brittle minerals and shale bedding seriously affect the mechanical performance of shale, and macroscopic mechanical experimental methods cannot separate these key factors for analysis. In this study, nanoindentation tests were conducted on clay and carbonate shales, and the effects of felsic minerals on the micromechanical characteristics of shale were evaluated. The shale indentation process was simulated using finite element software ABAQUS, and the effects of bedding morphology and mechanical parameters on stress diffusion and energy transfer were analyzed. The results showed that with the increase of felsic mineral content, clay shale exhibited brittle mineral depression in the indentation test, while carbonate shale exhibited obvious crack propagation and brittle fracture. The dimensionless brittleness indices of 4.405, 4.334, 6.178, and 7.117 for samples A1, A2, B1, and B2, respectively. Felsic minerals increase the brittleness of shale, but the influence of clay shale is relatively small. The influence of bedding morphology on shale indentation energy is relatively weak, while the mechanical properties of minerals determine the mechanical performance of shale. This article provides a microscale mechanical analysis of shale, and the research results can serve as an important supplement to macroscopic rock mechanics experiments. Combining the influence of brittle minerals on the mechanical performance of shale is helpful for further studying the mechanical characteristics of heterogeneous bedding shale reservoirs.