To accurately characterize the dynamic evolution of hydrate reservoir permeability under loading conditions, clay-rich, fine-silty hydrate-bearing sediments from the Shenhu area of the South China Sea were investigated. A series of permeability tests were performed under controlled stress conditions to elucidate both the mechanisms and the governing effects of hydrate saturation and effective stress on sediment permeability. The results show that a negative correlation between permeability and hydrate saturation is observed, alongside a pronounced decrease in permeability with increasing effective stress. Moreover, the sensitivity of permeability to effective stress is found to diminish as hydrate saturation increased. Building upon the Masuda permeability calculation model, a modified model is developed to account for the synergistic influences of effective stress and hydrate saturation. This revised model provides high accuracy, offering a more reliable reflection of permeability variations and governing trends across different effective stress levels and hydrate saturations.