Infilling fractured rock masses are widely distributed in the deeply buried oil reservoirs and surrounding rocks of mine caves. The internal filling material has a great influence on the mechanical properties and seepage characteristics of fractured rock mass. In this paper, through theories and experiments, the mechanism of permeability changes of infilling fractured rock under a coupling condition is studied. In terms of theory, the fracture compaction effect coefficient δ is added to the classical matchstick model, and the volume strain principle is used to propose a permeability model for fractured rock. Furthermore, based on the Hertz contact theory, mineral particles are generalized into rigid spheres, and the mechanism of crack development between mineral particles under seepage pressure is analyzed. In terms of experiment, a true triaxial seepage test was carried out on rock-like specimens to obtain the change law of the permeability characteristics of fractured rock. The test results are largely consistent with the theoretical calculation results of the theoretical model, which verifies the applicability of the model proposed in this paper. After the loading failure of the specimen, the internal filling material was taken out and analyzed, and by observing the distribution of cracks on the surface, it is verified that the seepage pressure promotes the development of cracks in the filling fracture.