Water inrush is commonly encountered while tunnelling through a conductive fault fracture zone, and seriously affects the hydrogeological environment around the tunnel. This paper proposed a new method to predict water inflow during the water inrush. Firstly, a unified time-dependent constitutive model considering Darcy flow and non-Darcy flow in the fault fracture zone was established, and the numerical time-variant water inflow was analyzed. Secondly, the analytical prediction of time-variant water inflow was conducted, which was compared with the numerical results and the measured data. The numerical and analytical prediction method was found to be reliable for the water inflow into the tunnel through the conductive fault fracture zone. On this basis, a combined numerical-analytical method for predicting water inflow was proposed and a reasonable prediction range of water inflow was constructed. Furthermore, the modified time-variant water inflow prediction method was developed by incorporating the temporal and spatial variation in the hydraulic conductivity. The modified prediction range of water inflow can be more consistent with the measured water inflow. The results show that the prediction accuracy of water inflow can be improved by considering the depth effect of hydraulic conductivity in the fault fracture zone for this typical case.