Monitoring and understanding long-term fate and regenerative therapy of administrated stem cells in vivo is of great importance. Herein we report organic nanodots with aggregation-induced emission characteristics (AIE dots) for long-term tracking of adipose-derived stem cells (ADSCs) and their regenerative capacity in living mice. The AIE dots possess high fluorescence (with a high quantum yield of 25 ± 1%), excellent biological and photophysical stabilities, low in vivo toxicity, and superb retention in living ADSCs with negligible interference on their pluripotency and secretome. These AIE dots also exhibit superior in vitro cell tracking capability compared to the most popular commercial cell trackers, PKH26 and Qtracker 655. In vivo quantitative studies with bioluminescence and GFP labeling as the controls reveal that the AIE dots can precisely and quantitatively report the fate of ADSCs and their regenerative capacity for 42 days in an ischemic hind limb bearing mouse model.