Numerical modeling and scenario composition are needed to characterize the geological environment of the disposal site and analyze the long-term evolution of natural barriers. In this study, processes and features of the hydro-mechanical behavior of natural barriers were categorized and represented using the interrelation matrix proposed by SKB and Posiva. A hydro-mechanical coupled model was evaluated for analyzing stress field changes and fracture zone re-activation. The processes corresponding to long-term evolution and the hydro-mechanical mechanisms that may accompany critical processes were identified. Consequently, practical numerical methods could be considered for these geological engineering issues. A case study using a numerical method for the stability analysis of an underground disposal system was performed. Critical stress distribution regime problems were analyzed numerically by considering the strata’s movement. Another case focused on the equivalent continuum domain composition under the upscaling process in fractured rocks. Numerical methods and case studies were reviewed, confirming that an appropriate and optimized modeling technique is essential for studying the stress state and geological history of the Korean Peninsula. Considering the environments of potential disposal sites in Korea, selecting the optimal application method that effectively simulates fractured rocks should be prioritized.