Semiconductor quantum dots (QDs) hold increasing potential for cellular imaging both in vitro and in vivo. In this report, we aimed to study imaging of human embryonic stem (ES) cells labeled with quantum dots (QDs), and to evaluate the viability and pluripotency of human ES cells labeled with QDs. We used the Tat-QDs to label human ES cells, evaluated the cytoactivity of human ES cells labeled with QDs by CCK8 assay and Flow cytometer, and verified the pluripotency of human ES cells labeled with QDs by differentiated the human ES cells into hemangioblasts/blast cells and neural-like cells. The result illustrated that human embryonic stem (ES) cells were labeled with QDs and intracellular QD number was associated with the dose of QDs. Human ES cell viability, proliferation, and pluripotency were not adversely affected by QDs compared with non-labeled control cells. In summary, this is the first report showing the QDs labeled human ES cells could be differentiated into hemangioblasts/blast cells and neurallike cells. These results provide a promising tool for imaging stem cell therapy noninvasively in vivo.