Fluorescence imaging is a non-invasive imaging technique, which facilitates the visualization of sub-cellular components in cells with high sensitivity and selectivity. Up to now, only indocyanine green (ICG) has been approved as a diagnostic reagent for intravenous application. But the intrinsic disadvantage of ICG has spurred more research attention to exploit new fluorescent materials in imaging fields. In the last decade, many materials, including inorganic and organic materials, have been developed for fluorescence imaging. There are some reviews about fluorescence bioimaging. In this review, we will summarize and highlight the reported organic nanoparticles for noninvasive long-term bioimaging. According to the emitting mechanism, fluorescent nanoparticles obtained from fluorophores with aggregation-caused quenching and aggregation-induced emission features are discussed respectively. Finally, we come up with some key issues and challenges in the future and clinical translation.