Tunnel excavation in fractured rock masses will induce a strongly hydro-mechanical coupling effect, which may cause significant rock mass damage and water pressure perturbation. This paper establishes a hydro-mechanical model to analyze the rock damage and fracture deformation induced by the tunnel excavation and the sequential drainage phase in fractured rocks. Afterwards, the model is used to investigate the effect of fracture networks on the excavation-induced damage in different fracture networks. It was found that the proposed model can effectively simulate the tunnel excavation and drainage phases in rocks embedded with discrete fracture networks. The damage evolution, fracture deformation, and groundwater seepage were well-captured in the simulation. The fracture network was found to significantly affect the uniformity of stress distribution. The coupling effect of tunnel excavation and groundwater seepage caused high stress zones around the tunnel, and there was a significant correlation between local stress, fracture deformation and water pressure. The distribution characteristics of fracture networks played a leading role on the development of excavation-induced damage, which further influenced the formation and development of excavation disturbed zone and excavation damaged zone.