Soil and rock mixture (SRM) is complex geological material that frequently leads to ground collapses, landslides, and debris flows. The mechanical and hydraulic properties of SRM have consistently attracted extensive attention. However, due to the presence of both large and small rock blocks, both experimental investigations and traditional mesh based numerical methods face significant challenges in the accurate evaluation of SRM mechanical properties. The numerical manifold method (NMM) is an excellent choice for this purpose as it effectively overcomes obstacles to mesh generation of complex SRM. Before exploring the hydraulic properties of SRM by NMM, it is necessary to construct a random preserved structure model of SRM, where the rock blocks are randomly distributed in space under a seismic load, which is a primary cause of structural changes in SRM. Using an explicit iterative scheme called the continuous–discontinuous element method (CDEM), we simulated the redistribution of rock blocks in SRM under artificial or natural seismic loads. Finally, we concentrated on determining the influences of some factors on SRM permeability using three-dimensional numerical manifold method (3D-NMM).