A unique method for synthesizing a surface modifier for metallic hydrogen permeable membranes based on non-classic bimetallic pentagonally structured Pd-Pt nanoparticles was developed. It was found that nanoparticles had unique hollow structures. This significantly reduced the cost of their production due to the economical use of metal. According to the results of electrochemical studies, a synthesized bimetallic Pd-Pt/Pd-Ag modifier showed excellent catalytic activity (up to 60.72 mA cm−2), long-term stability, and resistance to COads poisoning in the alkaline oxidation reaction of methanol. The membrane with the pentagonally structured Pd-Pt/Pd-Ag modifier showed the highest hydrogen permeation flux density, up to 27.3 mmol s−1 m−2. The obtained hydrogen flux density was two times higher than that for membranes with a classic Pdblack/Pd-Ag modifier and an order of magnitude higher than that for an unmodified membrane. Since the rate of transcrystalline hydrogen transfer through a membrane increased, while the speed of transfer through defects remained unchanged, a one and a half times rise in selectivity of the developed Pd-Pt/Pd-Ag membranes was recorded, and it amounted to 3514. The achieved results were due to both the synergistic effect of the combination of Pd and Pt metals in the modifier composition and the large number of available catalytically active centers, which were present as a result of non-classic morphology with high-index facets. The specific faceting, defect structure, and unusual properties provide great opportunities for the application of nanoparticles in the areas of membrane reactors, electrocatalysis, and the petrochemical and hydrogen industries.