High-stress and complex geological conditions impose great challenges to maintain excavation stability during deep underground mining. In this research, large anisotropic deformation and its management by support system at a deep underground mine in Western Australia were simulated through three-dimensional finite-difference model. The ubiquitous-joint model was used and calibrated in FLAC3D to reproduce the deformation and failure characteristics of the excavation based on the field monitoring results. After modeling verification, the roles of mining depth also the intercept angle between excavation axis and foliation orientation on the deformation and damage were studied. Based on the results, quantitative relationships between key factors and damage classifications were presented, which can be used as an engineering tool. Subsequently, the performance of support system installation sequences was simulated and compared at four different scenarios. The results show that, first surface support and then reinforcement installation can obtain a better controlling effect. Finally, the influence of bolt spacing and ring spacing were also discussed. The outcomes obtained in this research may play a meaningful reference for facing the challenges in thin-bedded or foliated ground conditions.