In cell therapies and regeneration medicine, superparamagnetic iron oxide nanoparticles (SPIONs) have been developed as excellent magnetic resonance imaging (MRI) contrast agents for stem cell labeling and tracking due to their biocompatibility. Here, we designed a self-assembled peptide amphiphile (PA) replace the transfection agents. This PA was conjugated to the surfaces of SPIONs to label rat mesenchymal stem cells (MSCs), which enhanced the contrast and labeling effects. The labeled cells showed that peptide-SPIONs had improved internalization, efficiency and T2-weight relaxivity and were nontoxic to the MSCs. The results demonstrated that these self-assembled peptide-modified SPIONs are potential candidates to label MSCs for tracking stem cells using MRI in vivo.