This study compares the investigated water vapor diffusion coefficient in the neat polyurethane (PU) membrane, the silica–PU nanocomposite membrane, and two surface-modified silica–PU nanocomposite membranes. The silane first surface modifier is with an amine functional group known as N-[3-(trimethoxysilyl)propyl]ethylenediamine, while the second one is with an aniline functional group known as N-[3-(trimethoxysilyl)propyl]aniline. The enhancement of water vapor diffusivity values through the polymer nanocomposite is desirable for the membrane air dehumidification application. The diffusivities were calculated via molecular dynamics simulations at the temperature of 298.15 K. The Einstein's relationship known as the mean square displacement method was used to obtain the diffusivity for the membranes. The results showed a significant effect on the diffusivity of water vapor for the surface-modified silica–PU nanocomposite membrane as compared with the neat PU and the unmodified silica–PU nanocomposite membranes. For the amine-modified silica, the diffusion coefficient increased by 80.3% compared with the unmodified silica–PU nanocomposite membrane. On the other hand, the aniline-modified silica outperformed the amine-modified one in terms of the diffusion coefficient by 22.4%.