Thin Pd–40%Cu films were obtained via the classical melting and rolling method, magnetron sputtering, and modified with nanostructured functional coatings to intensify the process of hydrogen transportation. The films were modified by electrodeposition, according to the classical method of obtaining palladium black and “Pd–Au nanoflowers” with spherical and pentagonal particles, respectively. The experiment results demonstrated the highest catalytic activity (89.47 mA cm−2), good resistance to CO poisoning and long-term stability of Pd–40%Cu films with a pentagonal structured coating. The investigation of the developed membranes in the hydrogen transport processes in the temperature range of 25–300 °C also demonstrated high and stable fluxes of up to 475.28 mmol s−1 m−2 (deposited membranes) and 59.41 mmol s−1 m−2 (dense metal membranes), which were up to 1.5 higher, compared with membrane materials with classic niello. For all-metal modified membranes, the increase in flux was up to sevenfold, compared with a smooth membrane made of pure palladium, and for deposited films, this difference was manyfold. The membrane materials’ selectivity was also high, up to 4419. The developed strategy for modifying membrane materials with functional coatings of a fundamentally new complex geometry can shed new light on the development and fabrication of durable and highly selective palladium-based membranes for gas steam reformers.