Organic fluorescent probes have attracted attention for bioimaging due to their advantages, including high sensitivity, biocompatibility, and multi-functionality. However, some limitations related to low signal-to-background ratio and false positive and negative signals make them difficult for in situ target detection. Recently, organelle targeting self-assembled fluorescent probes have been studied to meet this demand. Most of the dye molecules suffer from a quenching effect, but, specifically, some dyes like Pyrene, Near-Infrared (NIR), Nitrobenzoxadiazole (NBD), Fluorescein isothiocyanate (FITC), Naphthalenediimides (NDI), and Aggregation induced emission (AIE) show unique characteristics when they undergo self-assembly or aggregation. Therefore, in this review, we classified the molecules according to the dye type and provided an overview of the organelle-targeting strategy with an emphasis on the construction of fluorescent nanostructures within complex cellular environments. Results demonstrated that fluorescent probes effectively target and localized inside the organelles (mitochondria, lysosome, and golgi body) and undergo self-assembly to form various nanostructures that possess bio-functionality with long retention time, organelles membrane disruption/ROS generation/enzyme activity suppression ability, and enhanced photodynamic properties for anticancer treatment. Furthermore, we systematically discussed the challenges that remain to be resolved for the high performance of these probes and mentioned some of the future directions for the design of molecules.