<p>This study utilizes nuclear magnetic resonance (NMR) technology, with low-porosity granite and medium-porosity red sandstone as the research objects. Standardized fractures were prefabricated via Brazilian splitting tests. Integrating three-dimensional laser topography characterization and in-situ low-field NMR monitoring, a series of coupled seepage-NMR tests were carried out under a confining pressure gradient of 3–15&#xa0;MPa to investigate the influence of microbially induced calcium carbonate precipitation technology on the seepage stability of fractured rocks. The research reveals that the microbial reinforcement effect is governed by the “roughness threshold effect”: There exists a critical range for the initial surface morphology of fractures (quantified by the root mean square roughness coefficient R_rms and the average roughness coefficient R_a), which governs the pore network reconstruction pathway dominated by microbially induced CaCO₃ precipitation, thereby resulting in distinct phenomena of permeability optimization or deterioration. The results indicate a roughness-dependent divergence in post-treatment seepage response: higher-roughness specimens more frequently exhibit permeability enhancement, whereas lower-roughness specimens more frequently exhibit permeability reduction. The associated interpretations are discussed based on the coupled evolution of permeability and NMR <i>T</i>₂ spectra (Abbreviation for the transverse relaxation time spectrum under single-fluid conditions, which is used to characterize the pore size distribution of rocks) under confining pressure. The coupled model established in this research offers certain references and guidance for the green reinforcement of deep fractured rock masses.</p>