Abstract: Clayey-silt natural gas hydrate reservoirs in the South China Sea exhibit loose and unconsolidated structures, heterogeneous pore structures, high clay mineral contents, and strong hydrophilicity. These characteristics complicate the gas–water two-phase flow process in porous media following hydrate decomposition, posing challenges for efficient development. This study examines the transport response of clayey-silt reservoir samples from the Shenhu area using gas–water two-phase flow experiments and CT scanning to explore changes in pore structure, gas–water distribution, and relative permeability under varying flow conditions. The results indicate that pore heterogeneity significantly influences flow characteristics. Gas preferentially displaces water in larger pores, forming fracture-like pores, which serve as preferential flow channels for gas migration. The preferential flow channels enhance gas-phase permeability up to 19 times that of the water phase when fluid pressures exceed total stresses. However, small pores retain liquid, leading to a high residual water saturation of 0.561. CT imaging reveals that these hydro-fractures improve gas permeability but also confine gas flow to specific channels. Pore network analysis shows that gas injection expands the pore-throat network, enhancing connectivity and forming fracture-like pores. Residual water remains trapped in smaller pores and throats, while structural changes, including new fractures, improve gas flow pathways and overall connectivity. Relative permeability curves demonstrate a narrow gas–water cocurrent-flow zone, a right-shifted iso-permeability point and high reservoir capillary pressure, indicating a strong "water-blocking" effect. The findings suggest that optimizing reservoir stimulation techniques to enhance fracture formation, reduce residual water saturation, and improve gas flow capacity is critical for efficient hydrate reservoir development.