Shale, as a reservoir rock, exhibits obvious anisotropy in its physical and mechanical properties. An in-depth understanding of its mechanical behaviors considering the pre-existing cracks is vital for the extraction of oil and shale gas. This study develops a three-dimensional discrete element model incorporating initial cracks to analyze nonlinear crack-closure behavior under uniaxial compression. The results show that the nonlinear crack-closure and failure behaviors of shale are greatly affected by the anisotropic angle (β), microcrack density and width in rock matrix. Compared with the specimen without considering initial cracks, regardless of β, the specimen considering initial cracks are characterized by a lower crack-initiation stress, which is consistent with the evolution of microcracks formed in specimen.