To improve the performance of hydrogen-permeable alloys, quantitatively elucidating the metal–hydrogen interactions and identifying the controlling factors that govern the bottleneck step of the hydrogen permeation process are essential. In this study, based on the density functional theory, we characterized the interactions of hydrogen with point defects (such as antisite atoms and vacancies) in B2-type non-stoichiometric PdCu alloys, which are promising candidate materials for low-temperature working membranes for hydrogen purification. We proposed a “double defect” mechanism that produces a new type of defect complex with an atomic configuration similar to the Cu vacancy in B2-type PdCu alloys. We found that both Cu vacancies and double defects can act as strong hydrogen-trapping sites and are thus responsible for the marked decrease in hydrogen diffusivity. In contrast, antisite Cu atoms only repel H atoms and do not significantly hinder hydrogen diffusion. Whereas the binding energy of hydrogen to Cu vacancies and double defects exceeded 0.3 eV when relatively few (one or two) H atoms were trapped, the binding energy of hydrogen to Pd vacancies was substantially smaller (0.02 eV at most). Therefore, in Cu-rich non-stoichiometric PdCu alloys, the double defects may be the major hydrogen trapping sites. Furthermore, the effects of hydrogen on the formation of Pd vacancies, Cu vacancies, and double defects in B2-type PdCu alloys were clarified. Notably, double-defect formation from Pd vacancies in B2-type PdCu was significantly enhanced by the presence of nearby H atoms. This phenomenon, in which vacancies in B2-type intermetallic compounds transform into defect complexes in the presence of hydrogen, is postulated for the first time in this study. The findings of this study contribute to further understanding the driving forces for the formation of vacancy-hydrogen complexes in PdCu alloys at the atomic level and provide theoretical support for identifying the lattice defects that inhibit hydrogen permeability in Pd-based membranes.