Carbon dioxide (CO₂) geosequestration is a critical technology for reducing greenhouse gas emissions, with shale caprocks, such as Opalinus Clay (OPA), serving as essential seals to prevent CO₂ leakage. This study employs computational fluid dynamics and finite element analysis to investigate the hydromechanical behavior of OPA during CO₂ injection, integrating qualitative and quantitative insights. Validated numerical models indicate that capillary forces are the most critical factor in determining the material’s reaction, with an entry capillary pressure of 2–6 MPa serving as a significant threshold for CO₂ breakthrough. The numbers show that increasing the stress loading from 5 to 30 MPa lowers permeability by 0.3–0.45% for every 5 MPa increase. Porosity, on the other hand, drops by 9.2–9.4% under the same conditions. The OPA is compacted, and axial displacements confirm numerical models with an error margin of less than 10%. Saturation analysis demonstrates that CO₂ penetration becomes stronger at higher injection pressures (8–12 MPa), although capillary barriers slow migration until critical pressures are reached. These results demonstrate how OPA’s geomechanical stability and fluid dynamics interact, indicating that it may be utilized as a caprock for CO₂ storage. The study provides valuable insights for enhancing injection techniques and assessing the safety of long-term storage.