During the self-healing process of Bacillus subtilis biofilms on a solid MSgg substrate, large-scale ordered clusters emerge within the biofilm, providing an invasive advantages. To investigate the self-healing mechanism, an agent-based model is employed to simulate the self-healing processes of biofilms at two ages. The study reveals that a uniform cell distribution facilitates the healing of biofilm incisions. The nutrient diffusion rate within the biofilm and the elastic modulus (comprising cell and EPS) play a dominant role in the healing of circumferential incisions, while the diffusion rate outside the biofilm governs the healing of radial and penetrating incisions. These influencing factors can adjust cellular ordering, providing valuable insights for controlling the self-healing of Bacillus subtilis biofilms.