Grouting is a widely used method to seal and/or reduce hydraulic conductivity of fractured rock masses around underground structures. Recently, the efficient and effective grouting has been required from environmental and economical points of view. However, injection parameters such as injection pressure and water/cement ratio (W/C) are usually determined empirically by technical experts, because the filtration and penetration mechanism of cement-based grout have not been clarified sufficiently yet due to complicated physical and chemical processes of grout. In this paper, to better understand 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. The interaction between fluid and particles was evaluated by using immersed boundary (IB) method. The simulation results were compared with the laboratory injection test so-called "short slot" experiment to verify the applicability of the newly developed CFD-DEM code. The simulation results agree qualitatively well with experiments and the filtration and clogging process during cement-based grout injection was successfully reproduced by the CFD-DEM. Moreover, the effect of the injection pressure, W/C and particle size distribution on the filtration and penetration mechanism of grout was significant.