Deep disposal facility for High-Level radioactive Waste (HLW) uses a multi-barrier system to prevent the leakage of radionuclide. As a part of the engineered barrier, bentonite is primarily considered as the main buffering material. This is due to the adsorption and swelling properties of the bentonite, which are expected to effectively impede leakage of the radionuclide. In many cases, adsorption is generally regarded as occurring only within the buffer zone. However, several research has been conducted to explore the possibility of bentonite intrusion into the Excavation- Damaged Zone (EDZ) generated during excavation processes, because of the swelling properties of the bentonite. Generally, for host rock near the deep disposal facility such as granite, groundwater flows through the fracture network. Therefore, analysis of the characteristics of the fracture network is essential for predicting the behavior of radionuclide in groundwater. Accordingly, the bentonite intrusion into the fracture network is critical for safety assessment of the deep disposal facility. To analyze this, hydro-geochemical model was established utilizing COMSOL Multiphysics and PHREEQC, observing changes of the behavior of U (VI) along fracture network due to the swelling of bentonite. Modeling was conducted with progressively changing intrusion depth of the bentonite. According to the results, the behavior of U (VI) exhibited significant changes depending on the connectivity of the fractures. Based on the distribution characteristics of the fracture network, heterogeneous groundwater flow was observed. U (VI) was transported through the preferential pathway, which indicates high connectivity, due to the rapid groundwater flow. Notably, when changing the intrusion depth of bentonite, significant differences in behavior of U (VI) were observed in the 0-20 cm case. In contrast, as the intrusion depth increased, it was observed that differences became less evident. These results indicate that changes in the properties of fracture network in EDZ due to the swelling of bentonite significantly influence the behavior of U (VI).