To investigate the mechanism of water and mud inrush in water-rich fault fracture zones, a large-scale indoor water and mud inrush test system considering mass transfer and geostress state is developed. The simulation test of water and mud inrush disasters evolution process in the fault fracture zone with different hydraulic loading modes and medium parameters of fracture zones are carried out using the device. Some findings are as follows: 1) Evolution of water and mud inrush disasters in fault fractured zones is a strong coupling process of seepage and erosion. In the beginning, fine particles in the filling of fracture zones will migrate under the water pressure. Then, with the continuous migration and loss of fine particles, the flow pattern changes from laminar flow to turbulent flow, which eventually leads to water and mud inrush disasters. 2) The larger initial porosity of the filling in the fractured zone and the higher applied water pressure will induce the water inrush more easily. As a result, the evolution characteristics of seepage exhibit more obvious in the test and the increase of seepage field parameters such as permeability, porosity, and Reynolds number is much faster. Therefore, evolution curves of the seepage field parameters suddenly increase. 3) The evolution characteristics of water and mud inrush are more obvious under the gradient loading than under a loading condition with constant water pressure, and the critical water pressure of water and mud inrush from the filling is smaller. A generalized model of permeability evolution characteristics of the fault is established with analysis of flow state transition based on the relationship between water flow rate and time (Q?t), the relationship between hydraulic gradient and water flow rate (i?Q), and the relationship between permeability and hydraulic gradient (k?i) that describes the evolution characteristics of permeability. The results provide guidance for evolution mechanisms and prevention measures of water and mud inrush disasters in fault fractured zones.