By virtue of the good biocompatibility, outstanding fluorescence property, easy processability and functionalization, promoted photosensitizing efficiency, as well as facile construction of multi-modality theranostics, NIR-II fluorophores with aggregation-induced emission (AIE) characteristics exhibit inexhaustible and vigorous vitality in the fields of bioimaging and phototheranostics. We developed a series of novel NIR-II fluorescent materials with AIE features, and their unique advantages over traditional chromophores were demonstrated. The structure-function relationships of these AIE luminogens (AIEgens) for subcellular organelle-targeting, photosensitizing and bacterial discrimination were illustrated. In addition, these organic AIEgens have been successfully utilized for both diagnosis and phototherapeutic treatment of tumor and bacterial infection in vivo.