Deep Tunnel system is a large-scale urban flood control facility installed underground in order to reinforce the lack of drainage systems in developed cities. In a structure like a deep tunnel system, the undular bore generated in the downstream causes a problem in the hydraulic stability of the tunnel. In this study, to investigate the influence of the undular bore on the hydraulic stability at the “Shinwol rainwater storage and drainage system”, under construction for the first time in the country, a hydraulic model experiment was conducted on various flooding inflow scenarios. As a result of the hydraulic model experiment carried out in this study, the undular bore generated downstream is trapped in the pipe while moving to upstream, pushes the compressed air. It is judged that overflow occurred by choking the vertical drop shaft in the process when this compressed air is being exhaust through the upstream vertical drop shaft and blocking flood inflow. In addition, the analysis of velocity of undular bore shows that the undular bore transfers energy, and at this time, the pressure rose in the pipe and the velocity increment occurred of the undular bore. Further studies are needed to predict the size and velocity of undular bore, which plays an important role in the hydraulic stability of the tunnel in the deep tunnel system.