Stem cell-based therapy has emerged as a promising alternative therapeutic approach for acute stroke treatment due to its longer therapeutic time window as compared to the gold standard of administration of thrombolytic agent (tissue plasminogen activator). Bone marrow stromal cells (BMSCs) has garnered interest to act as a source of cell for stem cell therapy due to the promising beneficial structural and functional therapeutic outcome from transfusion of BMSCs as stroke treatment. Thus, it is highly desired to label BMSCs for long-term tracking in order to understand the fate of BMSCs after transplantation through reliable imaging technique for therapeutic evaluation. The emerging of fluorogens aggregation-induced emission characteristics (AIEgens), which emits bright fluorescence in aggregation state provides a promising alternative of conventional agents for the long-term cell labelling and tracking. Our group and others have successfully proven that with the help of the organic nanoparticles with bright fluorescence, excellent photostability and good biocompatibility, the nanoparticles (NPs) show good internalization in BMSCs with stable in vitro tracking ability up to 10 days in a rat photothrombotic ischemia (PTI) model. Ex vivo observation on day 7 after transplantation indicates that the BMSCs could migrate to and accumulate at the stroke site which was detected with strong fluorescence signal for the tracking of the BMSCs.