Concrete cracks have an adverse effect on the strength properties and durability of concrete structures. Therefore, repairing concrete cracks to recover the concrete’s strength parameters is an important task in the civil engineering field. For repairing concrete cracks, the MICP technique has been widely analyzed in recent times; however, no research has been conducted to deeply investigate the repair effects of MICP on concrete cracks with a rough surface using a theoretical model. In the current research, MICP with a novel mathematical model was conducted considering the precipitation of calcium carbonate (CaCO3), ureolysis, suspended biomass, geochemistry, transport of solutes, and biofilm growth. Furthermore, crack repair experiments were performed to assess the performance of the new mathematical model. The results revealed that the calculated concentrations of suspended biomass in cracks gradually decreased during the test. The comparison between the experimental results and calculated results verified the precision of the migration behavior of the suspended biomass. At the inlet, the solute concentrations and volume fractions of biofilm were higher, causing an increase in the productive rates of calcium carbonate. The consumed concentrations of solutes were higher for cracks with a smoother surface, eventually leading to smaller values of sonic time; the upper parts of the cracks also had smaller values of sonic time, showing good repair effects. The proposed mathematical model provides a better solution to control the repair time and microbial metabolism process, allowing for adjustive bioremediation and biomineralization of concrete, which could provide a firm basis for the remediation of materials in the civil engineering field.