We report a general method for preparing nanoparticle clusters (NPCs) in an oil-in-water emulsion system mediated by cetyl trimethylammonium bromide (CTAB), where previously only individual nanoparticles were obtained. NPCs of magnetic, metallic, and semiconductor nanoparticles have been prepared to demonstrate the generality of the method. The NPCs were spherical and composed of densely packed individual nanoparticles. The number density of nanoparticles in the oil phase was found to be critical for the formation, morphology, and yield of NPCs. The method developed here is scalable and can produce NPCs in nearly 100% yield at a concentration of 5 mg/mL in water, which is approximately 5 times higher than the highest value reported in the literature. The surface chemistry of NPCs can also be controlled by replacing CTAB with polymers containing different functional groups via a similar procedure. The reproducible production of NPCs with well-defined shapes has allowed us to compare the properties of individual and clustered iron oxide nanoparticles, including magnetization, magnetic moments, and contrast enhancement in magnetic resonance imaging (MRI). We found that, due to their collective properties, NPCs are more responsive to an external magnetic field and can potentially serve as better contrast enhancement agents than individually dispersed magnetic NPs in MRI.