The accurate prediction of groundwater inflow in tunnels in karst regions has been a difficult problem to overcome for a long time. This study proposes an equivalent fracture model that takes into account unsaturated seepage and fracture deformation to predict tunnel water inflow, which is constructed based on the TOUGH-FLAC3D framework. The proposed model with complete failure mechanisms of fracture, including shear failure and tensile failure, was applied to predict the water inflow of the Jianxing Tunnel in Guizhou Province to verify its effectiveness. The results indicate that the proposed numerical model was found to be comparable to on-site observations in predicting inflow rate. The inflow rate in a fractured network reaches a steady state faster than that in a non-fractured network. There is a significant difference of 100 times between the highest transient rate and the stable rate between the fracture network and the non-fractured model. The excavation-induced stress redistribution resulted in slip fracture occurring within a distance of approximately 8.2 m from the tunnel wall, which can increase the fracture width and in turn increases the amount of water flowing into the tunnel by about 50%. In addition, this paper also analyzes the impact of the factors of fracture density, incline angle, stress anisotropy, and initial fracture width on the inflow rate during tunnel construction. The study emphasizes the significance of considering deformable fractures and provides valuable insights for improving numerical tools for inflow prediction during tunnel construction.