We report the application of a versatile diblock copolymer, poly(ethylene oxide)-b-poly(γ-methacryloxypropyl trimethoxysilane) (PEO-b-PγMPS), to prepare nanocrystals such as iron oxide nanoparticles or quantum dots, with either a single core or multi-core cluster, for biomedical applications. This amphiphilic copolymer comprises both a hydrophilic PEO segment and a hydrophobic segment with a "surface anchoring moiety" (the silane group) which can interact effectively with the hydrophobic nanocrystals through ligand exchange. One of the unique features of this work is that we can control the formation of either single core nanoparticles or multi-core nanoclusters by simply varying the conditions of ligand exchange and aging of the mixture of block copolymer and nanoparticles without needing to change the copolymer. The morphologies of the resulting single core nanoparticles or multi-core nanoclusters were confirmed by dynamic light scattering and transmission electron microscopy. The clustered nanoparticles exhibit enhanced physicochemical properties that are beyond those expected from a simple accumulation of individual nanoparticles. Additionally, the hybrid nanoparticles containing both magnetic iron oxide nanoparticles and optical quantum dots obtained using our strategy provide have combined magnetic and optical functionalities that allow for potential new and expanded biomedical applications, as demonstrated by their use for magnetic resonance imaging and biomarker-targeted cell imaging.