Microbially induced calcium precipitation is a promising method for sealing fractures in low-permeability reservoirs, yet the role of anaerobic indigenous microorganisms under reservoir conditions remains unclear. In this study, reservoir samples were anaerobically enriched, and a urease-producing indigenous strain identified as Bacillus megaterium was isolated. Its growth, environmental tolerance, stimulation response, biomineralization products, and fracture-sealing performance were systematically evaluated. The strain showed good adaptability to fractured reservoir conditions and produced extracellular polymeric substances that promoted calcium enrichment and calcite formation. Visual fracture experiments demonstrated that microbial cementation significantly reduced fracture permeability and achieved effective sealing. The results further indicate that the dominant sealing mechanism depends on fracture aperture: surface adsorption controls sealing in narrow fractures, whereas particle deposition, settling, and migration become increasingly important in wider fractures. These findings clarify the fracture-sealing mechanisms of indigenous anaerobic microorganisms and support their potential application in subsurface permeability control.