Microbially Induced Calcium Carbonate Precipitation (MICP) technology has gained widespread attention in recent years, as an effective strategy for sealing rock fracture, reducing the permeability and improving the strength. However, the CaCO3 generated by MICP has complex precipitation patterns, and specialized numerical models considering the complex restoration mechanisms are rarely developed. In this paper, we propose a 3D Discrete Element Method (DEM) scheme with wall elements representing the surfaces of rock fractures and fines as cementing agents representing the CaCO3 crystals filling the fracture. After model calibration, the numerical results agree well with the experimental data in terms of global mechanical performance. The analyses in failure pattern suggest that the gradual reduction in global stiffness and the marginal change in strength as the fracture aperture increases is related to the transition from interface-dominated to filler-dominated responses.