Groundwater inrush during excavation is one of the greatest challenges in modern underground engineering. The characteristics of groundwater inrush induced by high-pressure water in fractured rocks are poorly understood, and the risk assessment of water inrush hazard associated with deep geological conditions remains to be improved. Here, we present an in situ high-pressure fluid injection experimental investigation of the hydraulic properties of deep natural fractured rocks. We observe that the injection rate increases as a nonlinear function of the injection pressure, and the process can be divided into an initial flow phase and a flow mutation phase, which indicates flow regime variations during fluid injection. Fluid injection primarily triggers fracture dilation and then results in an evident increase in rock permeability. A conceptual model involving multiple physical processes is derived to describe the permeability evolution and flow behavior of fractured rocks throughout the high-pressure fluid injection tests. The results provide valuable insight for evaluating the evolution of the hydraulic properties of the surrounding rocks in relation to water inrush and dewatering designs.