Herein we firstly reported the effects of generation 5 polyamidoamine dendrimerfunctionalized fluorescent multi-walled carbon nanotubes(dMNTs) on mice embryonic stem cell line CCE. The dMNTs were prepared and characterized, and incubated with murine ES CCE cells for 1 to 5day. These ES cells were observed by fluorescent microscopy, and were analyzed by flow cytometer and MTT. Results showed that the dendrimer-functionalized fluorescent multi-walled carbon nanotubes were successfully synthesized, could enter into ES cells quickly, more than 20μg/ml dose caused ES cells become smaller and smaller as the incubation time increased, and inhibited cell growth in dose- and time-dependent means, less than 5 μg/ml dose improves ES differentiation. These results demonstrate that dMNTs are toxic to ES cells at large dose, can induce ES cells' differentiation at small dose. The prepared dMNTs may be a highly efficient gene delivery system for ES cells, have potential applications in ES research.