Water inrush disasters continue to plague the advancement of deep underground mining activities. A better understanding of the structural integrity of fragmented geological bodies is crucial to ensuring mining safety. The objective of this study was to accurately reflect the dynamic evolution of pore structure changes and seepage channels in fragmented coal and rock mass of actual goafs under the coupling effect of mining stress and seepage. The co-evolution laws of the axial strain, nonlinear porosity, and permeability of fragmented coal and rock mass under different particle sizes, gradation characteristics, and stress states were compared, and a stress-pore-water seepage coupling model of the fragmented coal and rock mass was constructed. When subjected to the same axial pressure, the saturated fragmented coal exhibited a higher water permeability than the saturated fragmented rock mass. The greater the particle size, the higher the water permeability of fragmented coal and rock mass. The higher the gradation index, the higher the water permeability of these masses. Their porosity and axial pressure satisfied an exponential attenuation function, whereas their water permeability and axial pressure satisfied the Boltzmann function. The research results can provide theoretical support for preventing and controlling water inrush in goaf areas.