As a key hydrogeological parameter, soil permeability is considered significant for stratum stability analysis. The incorporation of biochar is known to alter soil structure and further influence its permeability. Biochar derived from bagasse was prepared, and permeability tests, NMR (nuclear magnetic resonance), and SEM (scanning electron microscopy) were conducted to comprehensively analyze the influence of biochar incorporation on the permeability coefficient of red clay and its underlying mechanisms. The experimental results show that the permeability coefficient of red clay is significantly affected by biochar incorporation. When the biochar content is less than 5%, the permeability coefficient decreases sharply with increasing biochar content. The preparation conditions of biochar (e.g., pyrolysis temperature and duration) are observed to influence its structure and properties, but their effects on the permeability of red clay are not significant. NMR and SEM analyses demonstrate that biochar incorporation modifies the soil pore size distribution, primarily through a reduction in the proportion of large pores. Additionally, the complex pore structure caused by biochar incorporation increases the tortuosity of seepage paths, thereby reducing the permeability of red clay. This study provides a theoretical basis for improving the permeability of red clay and offers new insights for enhancing stratum stability in engineering practices.