Fine particle internal erosion involves the detachment, transport, and deposition of fine particles within soil, significantly impacting agriculture, engineering, and environmental protection. Microbially induced calcite precipitation (MICP) has proven to be an effective method for controlling internal erosion. To optimize MICP protocols for effective erosion control, understanding the microscopic mechanisms by which MICP reduces fine particle erosion is essential but remains unclear. In this study, microfluidic chip experiments were conducted to observe the characteristics of calcium carbonate crystals and fine particles before and after MICP reinforcement and erosion. Through quantitative analysis of the calcium carbonate produced by MICP and eroded fine particles, the effects of bacterial density, concentration of cementation solution, and flow rate on the efficiency of MICP in resisting soil internal erosion were investigated. In addition, three primary mechanisms by which MICP reduces fine particle erosion were identified. Firstly, in situ sand stabilization occurs when calcium carbonate generated by MICP bonds and encapsulates fine particles, forming larger particles that remain stable under erosive flow conditions. Secondly, regional sand stabilization is achieved as MICP-produced calcium carbonate crystals narrow or block the flow channels, preventing extensive migration of fine particles. Lastly, adjacent particle stabilization is facilitated by calcium carbonate crystals, which remain stable during water flow erosion and alter the erosion flow lines, creating zones adjacent to the crystals where fine particle movement is minimized. These findings provide a deeper understanding of the role of MICP in erosion control and can inform the development of more effective erosion mitigation strategies.