Controlled self-assembly of magnetic nanocrystals has important applications in biomedical fields. In this study, hydrophobic superparamagnetic iron oxide (SPIO) nanocrystals are self-assembled into small clusters (mean diameter <100 nm) in water phase with the help of partially alkylated hyper-branched polycation, polyethylenimine (PEI). The amphiphilic PEI can wrap one or multiple SPIO nanocrystals inside micelle cores depending on different polycation/SPIO mass ratios. These SPIO nanocrystal containing micelles are superparamagnetic at room temperature. At the magnetic field of 1.5 T, single SPIO nanocrystal containing micelles have a T2 relaxivity of 118 Fe mM(-1)s(-1), while multiple SPIO nanocrystals micelles have relatively higher T2 relaxivities up to 323 Fe mM(-1)s(-1). Next, these potential magnetic resonance imaging (MRI) probes are tested for labeling rabbit mesenchymal stem cells. The formulation with a low polymer/SPIO ratio (0.2) is biocompatible and effective in labeling. Under a clinical MRI scanner, 3 x 10(6) labeled cells in gelatin phantom present much darker images than controlled ones. The T2 relaxation rate of the labeled cells is approximately 74.2 s(-1), significantly higher than the control cells of approximately 3.4 s(-1). This new amphiphilic polycation/SPIO nanocomposite may provide opportunities in cell labeling and tracking their behaviors in vivo.