The evolution of porosity and permeability of silty clay sediments in the South China Sea has significant effect on gas hydrate production due to the stress effect of submarine overburden rocks. The gas permeability of silty clay specimens under different effective stresses was measured in a cylindrical stainless steel reaction vessel. The experimental results in this paper show that application of effective stress destroys gas permeability of methane hydrate specimens. The power function relation between permeability and effective stress and exponential function relation between porosity and effective stress are given. The experimental data show that the formation of methane hydrate improves the compressible channel of montmorillonite deposits. The permeability damage rate increases with increase of effective stress, and stress sensitivity coefficient increases first and then decreases with increase of effective stress. Finally, an effective permeability equation of sediment containing hydrate saturation and effective stress parameters is established. The results are of guiding significance for the study of the stress dependence of porosity and permeability of gas hydrate silty clay reservoirs in the South China Sea. • Power law is superior to exponential law for showing permeability stress dependency. • Hydrate formation improves the compressible space of montmorillonite sediments. • Permeability damage rate increase with increasing effective stress in sediments. • Stress sensitivity coefficient show a trend of decreasing first and then increasing. • Relational expression between effective stress and permeability is proposed.