A cyclic peptide CC9 that targets cell membrane of mesenchymal stem cells (MSCs) is coupled with Gd-DOTA to yield a Gd-DOTA-CC9 complex as MRI contrast agent. It is used to label human MSCs (hMSCs) via electroporation. Electroporation-labeling of hMSCs with Gd-DOTA-CC9 induces cell-assembly of Gd-DOTA-CC9 nanoclusters in the cytoplasm, significantly promotes cell-labeling efficacy and intracellular retention time of the agent. In vitro MRI of labeled hMSCs exhibits significant signal reduction under T -weighted MRI, which can allow long-term tracking of labeled cell transplants in in vivo migration. The labeling strategy is safe in cytotoxicity and differentiation potential.