We report the size-controlled self-assembly of polymersomes through the cooperative self-assembly of nanoparticles and amphiphilic polymers. Polymersomes densely packed with magnetic nanoparticles in the polymersome membrane (magneto-polymersome) were fabricated with a series of different sized iron oxide nanoparticles. The distribution of nanoparticles in a polymersome membrane was size-dependent; while small nanoparticles were dispersed in a polymer bilayer, large particles formed a well-ordered superstructure at the interface between the inner and outer layer of a bilayer membrane. The yield of magneto-polymersomes increased with increasing the diameter of incorporated nanoparticles. Moreover, the size of the polymersomes was effectively controlled by varying the size of incorporated nanoparticles. This size-dependent self-assembly was attributed to the polymer chain entropy effect and the size-dependent localization of nanoparticles in polymersome bilayers. The transverse relaxation rates (r2) of magneto-polymersomes increased with increasing the nanoparticle diameter and decreasing the size of polymersomes, reaching 555 ± 24 s-1 mM-1 for 241 ± 16 nm polymersomes, which is the highest value reported to date for superparamagnetic iron oxide nanoparticles.