The important role of structure homogeneity in three-dimensional network nanostructures serving as noble metal aerogels (NMAs) has attracted extensive attention in the field of electrochemistry in the last two decades, whereas a comprehensive study of tailoring skeleton units and element distributions in NMAs is still lacking. Herein, a new modulation strategy to easily prepare multiscale NMAs with tunable composition is developed by utilizing the electrostatic interaction between oppositely charged colloidal metal nanoparticles. The modulation rule of the chemical distribution in bimetallic aerogels leads to the construction of the as-tailored double skeleton aerogels for the first time. Considering their specific structures, the intrinsic and exceptional catalytic and electrocatalytic performances of NMAs were investigated. This study optimizes the structure homogeneity of noble metal aerogels by investigating nanoparticle–ligand interactions and provides further proof of their exceptional electrocatalytic capabilities.