Magnetic nanoparticle clusters composed of primary magnetic nanoparticles can not only significantly enhance the magnetic properties of the assembly but also retain the superparamagnetic properties of the individual primary nanoparticle, which is of great significance for promoting the development of multifunctional advanced materials. Herein, water-soluble biocompatible and superparamagnetic europium-doped iron oxide nanoparticle clusters (EuIO NCs) were directly synthesized by a simple one-pot method. The obtained EuIO NCs have excellent water solubility, colloidal stability, and biocompatibility. Europium doping significantly improved the contrast enhancement effect of EuIO NCs in T 1-weighted MR imaging. In addition, EuIO NCs can be functionalized by active molecules, and the rhodamine123-functionalized EuIO NCs have long circulation time and excellent fluorescence imaging performance in vivo. This study provides a simple strategy for the design and construction of a novel multifunctional magnetic nanoplatform and provides solutions for the development of multimodal imaging probes and the diagnosis of disease.