Magnetic nanoparticles (MNPs) have many potential biomedical applications. Improvements in their magnetic properties and solubility are necessary for these applications to realize their full potential. In this study, MNPs in the form of raspberry-like magnetite (Fe3O4) nanoparticle clusters, consisting of tiny Fe3O4 particles with a diameter of approximately 20 nm, were prepared under hydrothermal conditions at 200 °C in the presence of 3,4-dihydroxyhydroxysinnamic acid (DHCA). The primary particles were connected by DHCA molecules to form the clusters, which were well dispersed in water media because a COOH group from DHCA appeared on their surfaces. The cluster size could be tuned from 50 to 400 nm without changing the primary particle size by controlling the reaction time. Therefore, all prepared clusters displayed superparamagnetic properties at room temperature. In addition, the sensitivity of Fe3O4 to an external magnetic field could also be controlled by the cluster size.