Water inrush accident into tunnel has become a bottleneck problem restricting the construction of deep-buried long tunnels, and the effect of intersecting faults on water inflow into tunnel is more complicated. Based on in-situ water pressure test data, the change law of the seepage characteristics in fault zone is analyzed, and an improved Darcy–Brinkman seepage model based on the theory of three-district zoning of faults is established. By assuming that the permeability coefficient conforms to the superposition principle, the underground seepage numerical model of intersecting faults that with perpendicular directions to tunnel is established. Then five calculation conditions are analyzed when the tunnel excavation axis is located at different relative height of the fault intersection center, so as to obtain the effect of the relative vertical location of the tunnel to the fault intersection center on the water pressure field, the seepage velocity field and the water inflow into tunnel. The results show that water inflow into tunnel crossing intersecting faults has litter relationship with the upper or lower position between the fault intersection center and the tunnel, but mainly depends on the relative height between them. The smaller the relative height, the smaller the water pressure, the greater the water inflow. Compared with the theoretical formula method and the stochastic mathematical method, the numerical simulation method can reflect the gradual process of water inrush while encountering intersecting faults in excavation and the change law of water inflow in different space and time under specific geological conditions, which is most consistent with the in-situ water inflow monitoring data.