Amphiphilic molecular brushes, i.e. graft copolymers (graft-CP), with a hydrophobic polyimide main chain and hydrophilic side chains of polymethacrylic acid at a high degree of polymerization m of the side chains and their grafting density, can be used as nanocontainers for the targeted delivery of drugs/agents. In this work, silver nanoparticles (Ag0) or selenium nanoparticles (Se0) in zero-valence form with a complex of unique biomedical properties were used as a loading agent. A comparative study of aqueous dispersions of Ag0 and Se0 nanoparticles stabilized by amphiphilic molecular brushes of varying topology was carried out using UV–visible spectroscopy, atomic force microscopy and transmission electron microscopy. The possibility of controlling the structural-morphological and spectral parameters of the Ag0/graft-CP and Se0/graft-CP nanostructures by changing the degree of polymerization m of side chains of the graft copolymer is shown.