Groundwater inrush through fault fracture zones is caused by small particle migration from fractured rocks of the faults. To investigate particle migration with the water flow, a 3D model was established for the solid-water two-phase flow. First, the simulated crushed sandstone was represented by certain different-sized particles with a novel cohesive force. The discrete element method (DEM) was applied for particles considering the cohesive force, the collisions, the friction, and other conventional forces. Second, the process of particle migrating from the crushed sandstone was simulated under multiple effects accompanied by some experiments. The results indicate that the migration characteristics vary with different-sized particles, and the mass loss for different-sized particles are high at the beginning leading to stabilized conditions at different times. It can be also found that the total mass loss rate and the final mass loss all increase with the increases of initial water velocity, while the final mass loss decrease with the increases of the axial force. Moreover, selected stimulation results were compared with the experimental results and the previous simulated results, and reasonable agreements could be obtained, which would provide consults for particle migration during groundwater inrush through fault fracture zones in underground engineering.