Membranes on palladium alloy basis with surface modified by nanoparticles with high catalytic activity are useful in deep hydrogen purification and single-stage process of high-purity hydrogen production. This paper reports the development and improvement of methods for synthesis of Pd-based pentatwinned nanoparticles of strictly specified morphology with certain shapes, facets and composition. The competing effect of surfactants and optimization of the halide ions ratio in solution make it possible to direct a particle growth towards formation of pentatwinned Pd-nanostars. Pd–23%Ag coatings synthesized on the surface showed uniquely high peak current density of up to 238 mA cm−2 in alkaline methanol oxidation reaction. This is due to both increased surface area and greater catalytic activity of nanostars’ facets. A record increase in hydrogen permeability of up to 12.5 mmol s−1 m−2 at 100 °C has been achieved for palladium-silver membranes with modified surface. This indicates an acceleration of sorption/desorption stages. The developed method for controlling morphology of nanoscale coatings opens the way to the production of membrane hydrogen filters, which operate at room temperature.