The innovative technology of microbially induced calcium carbonate precipitation (MICP) soil modification is widely used in soil reinforcement, soil remediation, environmental remediation and other fields, and has gradually become a hot research direction. Recent research is more focused on the overall physical and mechanical characteristics of the uniform reinforced specimen. There is limited research on the distribution characteristics of calcium carbonate along the seepage path during the reinforcement process. However, the distribution characteristics of calcium carbonate play a significant role in the physical and mechanical characteristics of the solid, especially in the large-scale MICP reinforcement process. In this study, based on the microbial mineralization reaction tests of different concentrations of cement solution at the laboratory sample scale, the calcium carbonate distribution on the surface of the sample at the microscale SEM observation and the CT scanning reconstruction of the micro pore structure characteristics of the microbial reinforced soil, we discussed the characteristics of the non-uniform reduction of calcium carbonate distribution and porosity in the process of microbial consolidation. Based on the Kozeny-Carman equation, the conceptual model of effective porosity was introduced, and the time relationship between porosity and calcium carbonate precipitation was considered to establish a bio-chemical-seepage multi-physics field coupling model. The precipitation of calcium carbonate in the axial direction of the model sample exhibits an uneven feature of more at the top and less at the bottom, and the distribution characteristics of porosity also show an uneven feature of more at the top and less at the bottom.