Stem cell therapeutics has emerged as a novel regenerative therapy for tissue repair in the last decade. However, dynamically tracking the transplanted stem cells in vivo remains a grand challenge for stem cell-based regeneration medicine in full understanding the function and the fate of the stem cells. Herein, Ag2S quantum dots (QDs) in the second near-infrared window (NIR-II, 1.0-1.4 m) are employed for dynamically tracking of human mesenchymal stem cells (hMSCs) in vivo with high sensitivity and high spatial and temporal resolution. As few as 1000 Ag2S QDs-labeled hMSCs are detectable in vivo and their fluorescence intensity can maintain up to 30 days. The in situ translocation and dynamic distribution of transplanted hMSCs in the lung and liver can be monitored up to 14 days with a temporal resolution of 100 ms. The in vivo high-resolution imaging indicates the heparin-facilitated translocation of hMSCs from lung to liver as well as the long-term retention of hMSCs in the liver contribute to the treatment of liver failure. The novel NIR-II imaging offers a possibility of tracking stem cells in living animals with both high spatial and temporal resolution, and encourages the future clinical applications in imaging-guided cell therapies.