Iridium(III) complexes have been shown to be promising probes in two-photon imaging to real-time track the transplanted cells in stem-cell-based therapy. Here, we report on polymeric nanocapsules loaded with red phosphorescence dye of bis(2-methyldibenzo[f,h]quinoxaline) (acetylacetonate) iridium(III) (Ir(MDQ)2acac) with excellent stability created by the double emulsion method. The Ir(MDQ)2acac nanocapsules present high biocompatibility and an efficient fluorescent labeling rate when incubated with cultured mouse neural stem cells (NSCs). More importantly, the Ir(MDQ)2acac nanocapsules had both one- and two-photon imaging properties with stable phosphorescence lasting for 72 h. Furthermore, data from in vivo tracking in nude mice demonstrated that the photoluminescence from Ir(MDQ)2acac nanocapsules in NSCs could be stably monitored for up to 21 days. Our data shed light on the potential clinical application of iridium complexes encapsulated in polymeric nanospheres for two-photon imaging in real-time tracking of the transplanted stem cells.