Grouting is a widely used method for sealing fractured rock masses around underground structures to reduce or stop groundwater inflow. One important aspect is the grout penetrability. However, the clogging and penetration mechanism of cement-based grout have not been clarified sufficiently yet due to complicated physical and chemical processes of grout, such as pressure-dehydration, consolidation, bleeding, clogging, absorption, sedimentation and condensation etc. Therefore, design and construction of grout injection depends on the experience of field technicians. Based on this situation, authors had developed a 2D numerical model of coupled Computational Fluid Dynamics and the Distinct Element Method (CFD-DEM), and simulate a laboratory scale grout injection experiment to better understand the penetration and clogging mechanism of cement-based grout. However, the results have raised some problems in this 2D approach. The flow of fluid and particles in the depth direction can not be represented in the two-dimensional simulation. Then, the simulated grout injection completely stopped instantaneously when particles formed an arch structure and clogging occurs. In actual grout injection test, the amount of cement that flows out from the outlet is reduced gradually and clogging occurs as a result. 3D simulations are essential in order to accurately reproduce the above experimental results. This paper presents 3D CFD-DEM simulations for the laboratory grout injection test (called "short slot" experiment) performed in Royal Institute of Technology (KTH) in Sweden. The simulation results agree qualitatively well with the actual experimental results, and the clogging process during the injection of cement-based grout was successfully reproduced by the 3D CFD-DEM code. The presented numerical model in this paper gives a better understanding for clogging and penetration mechanism of cement-based grout.