The pore structure of deep tight sandstone reservoir is complex and heterogeneous, and it is difficult to determine the influencing factors of pore microscopic parameters on the characteristics of gas-water phase permeability. In this paper, based on the fractal geometry theory, combined with the core Mercury intrusion porosimetry (MIP) method, nuclear magnetic resonance (NMR) T2 spectroscopy test and micron CT scanning results, the micro-pore throat parameters and various scale fractal dimensions of the reservoir are obtained. Through the mobile gas porosity and the maximum atmospheric phase relative permeability, the control mechanism of the fractal dimension and micro-pore throat structure parameters on the gas-water phase permeability characteristics is discussed. The results show that mercury injection and NMR fractal curves have obvious "three-stage" characteristics, and the total shape dimension of the reservoir describes the distribution of seepage and movable fluid more accurately when gas and water coexist. The maximum mercury saturation, average pore throat radius, total reservoir shape dimension and displacement pressure have significant effects on the mobile gas porosity during gas seepage. The average pore throat radius has a significant influence on the maximum effective gas phase relative permeability in gas seepage. The control mechanism of the micro-pore structure on the gas-water phase permeability can provide a powerful guide for the efficient development of water-producing gas reservoirs.