The mechanical and hydraulic behavior of clay in the excavation damaged zone (EDZ) around underground repository is relevant for the assessment of the safety of geotechnical barriers. By integrating Mohr-Coulomb criterion and damage mechanics considerations, an elasto-plastic damage model is established for clay stone. Based on laboratory and in site investigations, the hydro-mechanical coupled damage model and permeability healing model is developed by the fully coupled hydro-mechanical coupled model, which can predict permeability changes and fractures self-healing in EDZ. Considering the construction of connecting gallery of radioactive waste disposal in deep clay formation in Belgium, a finite element damage model for simulating shield tunneling is proposed. The variations of damage and permeability around the tunnel with time are analyzed in detail. The proposed model is able to effectively depict the main features of hydro-mechanical behaviors of Boom clay.