Grouting is a widely used method to seal and/or reduce permeability of fractured rock masses around underground structures. However, the filtration and penetration mechanism of cement-based grout have not been clarified sufficiently yet due to complicated physical and chemical processes of grouting. Therefore, the grout material and injection parameters such as injection pressure and water/cement ratio (W/C) are usually determined empirically by technical experts at the injection site. In this paper, for better understanding of the penetration and filtration mechanism of cement-based grout through rock fractures, the two-dimensional numerical model of coupled Computational Fluid Dynamics and the Distinct Element Method (CFD-DEM) was developed and the effect of rock fracture roughness on the filtration and penetration mechanism was numerically investigated. The simulation results clearly shows that the effect of surface roughness of rock fracture on the movement of cement particles and the amount of injected cement particles is significant.