Microbially induced calcium carbonate precipitation (MICP) technique shows significant potential for grouting and sealing micro-fractures in rock. However, its application is currently challenged by uneven precipitate distribution, where localized clogging can disrupt grouting continuity, compromise sealing reliability, and even introduce engineering safety risks. This study investigated the effects of grouting flow rate on permeability reduction and precipitate distribution characteristics during MICP-based fracture sealing using a self-designed fracture model apparatus. The experimental sequence followed analyzing the influence of flow rate on bacterial attachment efficiency, implementing mineralization grouting for fracture sealing, monitoring the permeability reduction process, and characterizing precipitate distribution through 3D scanning. The results indicate that an increase in grouting flow rate leads to a significant reduction in bacterial retention efficiency. Variations in grouting flow rate markedly affect the distribution patterns of precipitates in the fractures, and differences in the spatial distribution of precipitates further cause variations in the permeability reduction process. A flow velocity of 4.708 mm/s was identified as optimal, achieving both high grout utilization efficiency and effective sealing performance.