Amorphous silica typically has nano-sized pores with a narrow pore size distribution, which allows selective permeation of hydrogen from complex gas mixtures for cost-effective hydrogen purification after methane steam reforming processes. Despite many advantages, porous silica membranes exhibit poor stability in moist atmosphere, limiting their practical applications. Transition-metal doping is known to be effective in improving the hydrothermal stability of the silica membranes. By performing a series of simulations based on first-principles calculations, we elucidate the underlying mechanism of how transition-metal doping improves the hydrothermal stability of the porous silica membranes. Our calculation results highlight that transition-metal atoms added to the porous silica membrane serve as a softener to release the stress of the silica network at the severely deformed pore curvature. The diminished strain energy of the transition-metal-bound silica pore curvature in turn increases the thermodynamic energy barrier for the formation of mobile species required for pore size redistribution, ultimately leading to strengthened hydrothermal stability. This fundamental understanding can be an important theoretical basis for developing practically applicable high-durability silica-metal hybrid membrane materials.