Multiphoton microscopy is an exciting tool for biomedical research because it can be used to image single cells in vivo due to its greater penetration depth, lower phototoxicity and higher resolution when compared to confocal laser scanning microscopy. This helps researchers understand how certain cells change over time and evaluate the efficacy of different therapies. Herein, we report a new AIE luminogen (AIEgen), abbreviated as TPE-TETRAD, with a favorable absorption and efficient deep-red emission in the solid state. TPE-TETRAD possesses a high two-photon absorption cross-section (313 MG at 830 nm) and a rich array of non-linear optical properties including aggregation-induced three-photon luminescence. Biotinylated TPE-TETRAD nanoparticles are also fabricated and applied to stain mitochondria in live cancer cells with high specificity. The purpose of this study is to characterize a novel deep-red AIEgen and fabricate biotinylated nanoparticles for applications as (1) biocompatible and photostable AIE probes for specific mitochondria imaging and (2) multiphoton imaging probes suitable for two/three-photon fluorescence microscopy.