The water diffusion behaviors and activation energies of PDA-and ODA-based polyimide thin films were quite dependent on both the chemical structure and the morphological structure in the films. The water diffusion coefficients of polyimide thin films increased with increasing temperature. The activation energies varied in the range of 5.81 to 9.27 kcal/mol and were relatively higher for the PDA-based polyimide thin films than for the corresponding ODA-based polyimide thin films. For the PDA- and ODA-based polyimide films, the differences in the morphological structures and the chemical affinity to water molecules might be reflected directly on the water diffusion behaviors. The PDA-based polyimide films exhibited a relatively more ordered morphological structure (high crystallinity and good in-plane orientation) than that of the corresponding ODA-based polyimide thin films, which may serve as impenetrable obstacles for the water diffusion in the out-of-plane direction. Consequently, it may lead to a relatively slower water diffusion and high activation energy in the PDA-based polyimide thin films. Additionally, the PDA-based polyimide films with relatively lower chemical affinity showed relatively low diffusion coefficients and high activation energies.